Why does the baseline distance vary from line to line in my manyfoot paragraph style footnotes?

Question

I'm using package manyfoot to create paragraph style footnotes in my document. However, I'm puzzled, because the distance between baselines seems to vary from line to line in my footnote area. It's subtle, but noticeable:

For example, on the first page, there is less distance between the baselines of footnote lines 8 and 9, and between 9 and 10, than there are between most of the other lines on that page. The same is true for several of the lines on page 2.

Thus far, I've not been able to figure out why this is happening, so I thought I'd make a post and see if anyone notices anything obviously wrong that I'm doing.

Here's the complete source code, which I compiled with XeLaTeX using my MiKTeX distribution. It uses the standard MS Windows Times New Roman font.

%&program=xelatex
%&encoding=UTF-8 Unicode

% This will be a 9x6in book
\documentclass[11pt,openany]{book}

% Set up hyphenation
\usepackage[english,greek.polutoniko]{babel}

% Make sure these things are set before calling geometry
\setlength{\headheight}{16pt}
\setlength{\headsep}{0.125in}
\setlength{\footnotesep}{0.12in}
\setlength{\topskip}{0in}
\setlength{\footskip}{0.5in}
\setlength{\marginparsep}{0in}
\setlength{\marginparwidth}{0in}
\setlength{\marginparpush}{0in}

% Tables in Introduction
\usepackage{tabularx}
\usepackage{longtable}
\usepackage{setspace}
\usepackage[skip=-8pt,position=top,margin={0pt,0pt},justification=raggedright,textfont=bf]{caption}
\captionsetup{labelformat=empty}

% Use geometry package to set page size, margins, etc.
\usepackage[paperheight=9in,paperwidth=6in]{geometry}
\geometry{includehead,nofoot,twoside,top=0.5in,bottom=0.75in,left=1in,right=0.5in}

% Use this package to enlarge letters, etc.
\usepackage[dvipdfm]{graphicx}

% Used to enclose chapter numbers
\usepackage{wrapfig}
\setlength{\intextsep}{0pt}
\setlength{\columnsep}{1ex}

% Use "fancy header" package to make using alternating headers easy
\usepackage{fancyhdr}
\pagestyle{fancy}
\setlength{\footskip}{5pt}

% Footnote management
\usepackage[flushmargin,bottom]{footmisc}
\usepackage[para*,ruled,perpage]{manyfoot}
\usepackage{alphalph}
\DeclareNewFootnote{B}
\DeclareNewFootnote[para]{A}[alph]
\renewcommand{\thefootnoteA}{\alphalph{\value{footnoteA}}\hspace{0.1ex}}
\usepackage{fixfoot}
\setlength{\footnotesep}{1.1em}
\setlength{\footnotemargin}{0ex}

% Custom lettering for footnotes
\makeatletter
\def\alphalph@alph#1{%
  \ifcase#1%
    @%
  \or a\or b\or c\or d\or e\or f\or g\or h\or i\or j\or k\or l\or m%
  \or n\or o\or p\or q\or r\or s\or t\or u\or v\or w\or x\or y\or z%
  \else
    \AlPh@ctrerr
    @%
  \fi
}
\makeatother

% Allow hyphens in footnotes
\def\hyph{-\penalty0\hskip0pt\relax}

% Custom chapter head. This allows us to show the name of the chapter without
% having the unattractive "Chapter 1", etc., show up on the page.
\makeatletter
\def\@makechapterhead#1%
{%
    \vspace*{50\p@}%
    {%
        \parindent \z@ \raggedright \normalfont
        \interlinepenalty\@M
        \begin{center}%
            \Huge \bfseries #1\par\nobreak
            \vskip 40\p@
        \end{center}
    }%
}
\makeatother

% Redefine this to control table of content formatting. The only thing we really
% want from this is to format the table of contents chapter entries such that they
% do not have the chapter number in front of them. The line that generated the
% chapter number is still there, just like in the standard definition, but we
% have commented it out.
\makeatletter
\def\@chapter[#1]#2%
{%
    \ifnum \c@secnumdepth >\m@ne
        \if@mainmatter
            \refstepcounter{chapter}%
            \typeout{\@chapapp\space\thechapter.}%
            \addcontentsline{toc}{chapter}%
            {#1}%
        \else
            \addcontentsline{toc}{chapter}{\hspace{10mm}#1\dotfill}%
        \fi
    \else
        \addcontentsline{toc}{chapter}{\hspace{10mm}#1\dotfill}%
    \fi
    \chaptermark{#1}%
    \addtocontents{lof}{\protect\addvspace{10\p@}}%
    \addtocontents{lot}{\protect\addvspace{10\p@}}%
    \if@twocolumn
        \@topnewpage[\@makechapterhead{#2}]%
    \else
        \@makechapterhead{#2}%
        \@afterheading
    \fi%
}
\makeatother

% Use XeTeX scalable fonts
\usepackage{fontspec,newunicodechar}
\setmainfont{Times New Roman}
\newfontfamily\dropnum[Scale=2.8]{Times New Roman}

% Use this to allow intuitive if-then-else statements
\usepackage{ifthen}
\usepackage{xifthen}

% Use package for custom table of contents. This allows us to easily customize the table of
% contents, by, for instance, making it single-spaced and with dots after chapter listings.
\usepackage{tocloft}

% Smart spacing
\usepackage{xspace}

% Package for reserving space (lines) to make sure they don't get orphaned. We will use this
% to make sure that you don't see a section heading at the very bottom of a page by itself.
\usepackage{needspace}

% This package gives us dropped caps and numbers
\usepackage{lettrine}

\newcommand{\bookname}{}

% Custom chapter command. We just use this instead of \chapter so that we do not
% have to keep repeating the \fancyhead command after each call. The \fancyhead
% call places the English bible book name in the center of all headers.
\def\biblechapter#1#2#3#4%
{%
    \chapter[#1]{#2}%
    \renewcommand{\bookname}{#3}%
    \fancyhead[CE,CO]{\thepage}%
}

% Make sure that blank pages between chapters are really blank. This basically removes any
% header information from a page that ends up being generated as blank due to a chapter ending.
\makeatletter
\let\cleardouble@page\cleardoublepage
\AtBeginDocument%
{%
    \ifx\cleardouble@page\cleardoublepage
        \def\cleardoublepage{\clearpage
        {\pagestyle{empty}\cleardouble@page}}%
    \fi
}
\makeatother

% Set up as much as we can about headers and footers
\fancyhf{}
\renewcommand{\chaptermark}[1]{}
\renewcommand{\sectionmark}[1]{}
\fancyhead[RO]{\bookname\hspace*{0.5em}\leftmark}
\fancyhead[LE]{\bookname\hspace*{0.5em}\rightmark}

% Make a space between the text and the footnotes, and make a horizontal line all the way across.
% If the footnote text is too close to the main text, it looks bad. Also, because our footnotes
% are in paragraph format, it looks best with a rule that goes all the way across the page.
\makeatletter
\renewcommand\footnoterule%
{%
    \kern-2\p@%
    \hrule\@width\columnwidth%
    \kern2.6\p@%
}
\makeatother

% Use this counter to keep track of what Bible chapter we are in
\newcounter{BibleChapter}
\setcounter{BibleChapter}{0}

\newcommand{\LetterDrop}[2]{\lettrine[lines=2,findent=0em,nindent=0ex,loversize=0.1]{#1}{#2}}
\newcommand{\NumberDrop}[1]%
{%
    \begin{wrapfigure}{l}{0pt}%
    \dropnum{#1}%
    \end{wrapfigure}%
}

% Macro to mark the beginning of a new Bible book (e.g., Matthew, Mark, etc.)
% This macro sets the pagestyle to "empty" so that there will be no header on the first
% page of the Bible book. It also resets a counter to show what Bible chapter we are
% currently in (chapter is argument #1). It then displays the first letter of the
% first Bible chapter as an enlarged letter and marks the beginning of Bible chapter 1,
% verse one.
\def\bookbeg%
{%
    \thispagestyle{empty}%
}

% Set up macro to mark beginning of a new Bible chapter within a Bible book. Each
% Bible chapter must begin a new paragraph, but we do not want indentation because
% of the chapter number being a large numeral. We also restart the footnote
% counter so that footnotes begin again at "1" for this Bible chapter. We set the
% counter also that shows what Bible chapter we are in, and then we mark the current
% Bible chapter and verse.
\def\chapbeg#1%
{%
    \setcounter{BibleChapter}{#1}%
    \vskip 0.5em plus 0.1em minus 0.1em%
    \noindent%
    \NumberDrop{#1}%
}

% Set up a macro to begin a small (single chapter) book with a lettrine to begin
% instead of drop cap chapter number.
\def\smallchap#1#2{%
    \setcounter{BibleChapter}{1}%
    \markboth{1:1}{1:1}%
    \LetterDrop{#1}{#2}%
}

% Set up macro to mark beginning of a new Bible verse. We want to mark each verse with
% its verse number. The numbers will be either smaller, bold, and set slightly away
% from the beginning text of the verse, or smaller, raised slightly above the line,
% and flush with the text of the verse (almost). Note that if a section has just been
% printed, we don't want to add any horizontal space to the front of the verse number.
% That would cause unwanted "indentation".
\def\versebeg#1#2%
{%
    \ifthenelse{\equal{#2}{1}}%
    {%
    }%
    {%
        \raisebox{0.69ex}{\scriptsize{#2}}\hspace*{0.15em}\nobreak%
    }%
    \markboth{#1:#2}{#1:#2}%
}

\def\nbversebeg#1#2%
{%
    \setcounter{BibleChapter}{#1}%
    \raisebox{0.69ex}{\scriptsize{#2}}\hspace*{0.15em}\nobreak%
    \markboth{#1:#2}{#1:#2}%
}

\newlength{\parindentval}
\newlength{\parskipval}
\newlength{\hangindentval}

\newlength{\quoteindent}
\newlength{\versebox}
\setlength{\versebox}{\widthof{\footnotesize{22}\hspace*{0.1em}\nobreak}}
\setlength{\quoteindent}{1.2em}

\newcommand{\qverse}[2]%
{%
    \ifthenelse{\isempty{#1}}%
    {%
        \makebox[\versebox]{}%
    }%
    {%
        \makebox[\versebox]{\raisebox{0.15ex}{\footnotesize{#2}}\hspace*{0.1em}\nobreak}%
        \markboth{#1:#2}{#1:#2}%
    }%
}

\newcommand{\cnote}[2]%
{%
    \footnoteA{\textbf{#1}#2}%
}

% More condensed version of \parshape (https://tex.stackexchange.com/a/133660/5764)
\makeatletter
\def\newparshape{\parshape\@npshape0{}}
\def\@npshape#1#2#3{\ifx\\#3\expandafter\@@@npshape\else\expandafter\@@npshape\fi
  {#1}{#2}{#3}}
\def\@@npshape#1#2#3#4#5{%
  \ifnum#3>\z@\expandafter\@firstoftwo\else\expandafter\@secondoftwo\fi
  {\expandafter\@@npshape\expandafter{\the\numexpr#1+1\relax}{#2 #4 #5}{\numexpr#3-1\relax}{#4}{#5}}%
  {\@npshape{#1}{#2}}}
\def\@@@npshape#1#2#3{#1 #2}
\makeatother
% Temporarily adjusting the text width with paragraphs that extend to the following page (https://tex.stackexchange.com/a/472150/5764)
% Use cases for breaking a paragraph that is not visible to the end user, forcing the paragraph to be set with a full-width/-length
% last line. Then one could insert a \pagebreak if needed, depending on the layout requirements
\newcommand{\parnopar}[1][]{\parfillskip=0pt\par%
  #1%
  \parskip=0pt\noindent\parfillskip=0pt plus1fil}

\newsavebox{\dropcapbox}
\newcommand{\nbchapbeg}[1]{%
    \setlength{\parskipval}{\parskip}%
  \parnopar%
  \savebox{\dropcapbox}{\dropnum{#1}}%
  \newparshape
    {2}{\dimexpr\wd\dropcapbox+1ex}{\dimexpr\linewidth-\wd\dropcapbox-1ex}
    {1}{0pt}{\linewidth}\\%
  \noindent
  \llap{\raisebox{\dimexpr-\height+.55\baselineskip}[0pt][0pt]{%
    \usebox{\dropcapbox}%
    \hspace{1ex}%
  }}%
  \ignorespaces%
  \setlength{\parskip}{\parskipval}%
}

% Disable overfull box warnings
\hfuzz=15pt
\vfuzz=\hfuzz

% Eliminate warnings
\hbadness=10000
\vbadness=10000

% Prevent text from going into the right margin. Also, allow large stretches of the text
% to ensure that it is justified properly. This will look okay since our text is really
% split up with footnote markers anyway.
\setlength{\emergencystretch}{8em}

% Turn off hyphenation. Hyphenation of ancient Greek text does not look so good, and makes
% the text difficult to read for beginning readers.
\global\hyphenpenalty=200

% Prevent ugly widows and orphans. Nothing against widows and orphans though.
\widowpenalty=10000
\clubpenalty=10000

% Extract verse reference from a cnote
\makeatletter
\newcommand\VerseRef[1]{\@verseref#1 \@nil}%
\def\@verseref#1 #2\@nil{#1}
\makeatother

\newcommand{\mtOne}[1]{\normalfont{\huge\textbf{#1}}}
\newcommand{\mtTwo}[1]{\normalfont{\Large{#1}}}
\newcommand{\dashes}{{-}{-}{-}}

\newlength{\hangwidth}
\newcommand{\calchang}[1]{\settowidth{\hangwidth}{#1}}

\newcounter{thisfnmark}
\newcommand{\nextfnmark}[1]{%
  \setcounter{thisfnmark}{\value{footnoteA}}%
  \stepcounter{thisfnmark}%
  \footnotemarkA[\value{thisfnmark}]%
}

\newcommand{\poeticbegin}{%
    \vspace{0.6em}%
    \setlength{\parindentval}{\parindent}%
    \setlength{\parskipval}{\parskip}%
    \setlength{\parindent}{0em}%
    \setlength{\parskip}{0em}%
}

\newcommand{\poeticend}{%
    \setlength{\parindent}{\parindentval}%
    \setlength{\parskip}{\parskipval}%
    \vspace{0.6em}%
}

% Arguments:
%   #1: 1, 2, or 3 (poetry line level number)
%       #2: nobreakbefore, nobreakafter, or allowbreak (widow/orphan control)
%       #3, #4: chapter number, verse number
%       #5: leading characters that should extend left into the margin
%       #6: text to display as a line of poetry
\newcommand{\poeticline}[6]{%
    \ifthenelse{\equal{#2}{nobreakbefore}}{\nopagebreak}{}%                     % might need to prevent page break before last line of poetic section
    \par%
    \begingroup%                                                                                                            % new margins apply only locally within this group
    \setlength{\leftskip}{\versebox+3\quoteindent}%                                     % if poetry line wraps around, the wrap starts at this level of indentation
    \setlength{\parindent}{-\leftskip}%                                                             % negative indent each line of poetry all the way back to the left page margin
    \setlength{\rightskip}{\quoteindent}%                                                           % all poetry lines may extend to within this far of the right page margin
    \qverse{#3}{#4}%                                                                                                    % output either the verse number or an empty box the size of a verse number
    \hspace*{#1\quoteindent}%                                                                                   % now indent the line of poetry the appropriate amount given the level number
    \calchang{#5}%                                                                                                      % calculate left nudge if line starts with footnote marker or quotes
    \hspace*{-\hangwidth}%                                                                                      % perform the leftward nudge
    #6\relax%                                                                                                                   % output the poetic line itself
    \par%
    \endgroup%                                                                                                              % end the local margin group
    \ifthenelse{\equal{#2}{nobreakafter}}{\nopagebreak}{}%                      % might need to prevent page break after first line of poetic section
}

\setlength{\parskip}{0pt plus 0.02pt minus 0.1pt}

\begin{document}

\mainmatter
\flushbottom

\cleardoublepage
\cleardoublepage
\pagestyle{empty}

\biblechapter{Κατὰ Μᾶρκον}{\mtOne{ΚΑΤΑ ΜΑΡΚΟΝ}}{ΜΑΡΚΟΝ}{ΜΑΡΚΟΝ}
\bookbeg{}
\par{}\noindent{}\chapbeg{1}\versebeg{1}{1}Ἀρχὴ τοῦ εὐαγγελίου Ἰησοῦ Χριστοῦ, \cnote{1:1}{ υιου του θεου 98.2\%~¦~υιου θεου NA TH 0.5\%~¦~\dashes{} SBL WH 0.8\%}υἱοῦ τοῦ Θεοῦ.
\par{}\versebeg{1}{2}\cnote{1:2}{ ως~¦~καθως ECM\textsuperscript{†} NA SBL TH WH}Ὡς γέγραπται ἐν \cnote{1:2}{ τοις προφηταις 96.2\%~¦~τω ησαια τω προφητη CT 1.3\%}τοῖς προφήταις,
\poeticbegin{}
\poeticline{1}{nobreakafter}{}{}{}{Ἰδού, \cnote{1:2}{ εγω~¦~\dashes{} NA SBL TH WH}ἐγὼ ἀποστέλλω τὸν ἄγγελόν μου πρὸ προσώπου σου,}
\poeticline{2}{allowbreak}{}{}{}{ὃς κατασκευάσει τὴν ὁδόν σου \cnote{1:2}{ εμπροσθεν σου 96.6\%~¦~\dashes{} ECM\textsuperscript{†} NA SBL TH WH 3.3\%}ἔμπροσθέν σου.}
\poeticline{1}{allowbreak}{1}{3}{}{Φωνὴ βοῶντος ἐν τῇ ἐρήμῳ,}
\poeticline{2}{allowbreak}{}{}{}{Ἑτοιμάσατε τὴν ὁδὸν Κυρίου·}
\poeticline{2}{nobreakbefore}{}{}{}{εὐθείας ποιεῖτε τὰς τρίβους αὐτοῦ,}
\poeticend{}
\par\noindent{}\versebeg{1}{4}ἐγένετο \cnote{1:4}{ ιωαννης~¦~ιωανης WH}Ἰωάννης \cnote{1:4}{ βαπτιζων εν τη ερημω και 98.2\%~¦~ο βαπτιζων εν τη ερημω και NA TH 0.4\%~¦~ο βαπτιζων εν τη ερημω SBL WH 0.2\%}βαπτίζων ἐν τῇ ἐρήμῳ, καὶ κηρύσσων βάπτισμα μετανοίας εἰς ἄφεσιν ἁμαρτιῶν. 
\versebeg{1}{5}Καὶ ἐξεπορεύετο πρὸς αὐτὸν πᾶσα ἡ Ἰουδαία χώρα, καὶ οἱ \cnote{1:5}{ ιεροσολυμιται~¦~ιεροσολυμειται TH WH}Ἱεροσολυμῖται, \cnote{1:5}{ και εβαπτιζοντο παντες~¦~παντες και εβαπτιζοντο CT}καὶ ἐβαπτίζοντο πάντες \cnote{1:5}{ εν τω ιορδανη ποταμω υπ αυτου~¦~υπ αυτου εν τω ιορδανη ποταμω CT}ἐν τῷ Ἰορδάνῃ ποταμῷ ὑπ᾿ αὐτοῦ, ἐξομολογούμενοι τὰς ἁμαρτίας αὐτῶν. 
\versebeg{1}{6}\cnote{1:6}{ ην δε~¦~και ην CT}Ἦν δὲ \cnote{1:6}{ ο~¦~\dashes{} TR}ὁ \cnote{1:6}{ ιωαννης~¦~ιωανης WH}Ἰωάννης ἐνδεδυμένος τρίχας καμήλου, καὶ ζώνην δερματίνην περὶ τὴν ὀσφὺν αὐτοῦ, καὶ \cnote{1:6}{ εσθιων~¦~εσθων SBL TH WH}ἐσθίων ἀκρίδας καὶ μέλι ἄγριον. 
\versebeg{1}{7}Καὶ ἐκήρυσσε, λέγων, Ἔρχεται ὁ ἰσχυρότερός μου ὀπίσω μου, οὗ οὐκ εἰμὶ ἱκανὸς κύψας λῦσαι τὸν ἱμάντα τῶν ὑποδημάτων αὐτοῦ. 
\versebeg{1}{8}Ἐγὼ \cnote{1:8}{ μεν~¦~\dashes{} CT}μὲν ἐβάπτισα ὑμᾶς \cnote{1:8}{ εν 95\%~¦~\dashes{} ECM NA SBL WH 4.3\%}ἐν ὕδατι· αὐτὸς δὲ βαπτίσει ὑμᾶς \cnote{1:8}{ εν 99.7\%~¦~\dashes{} WH 0.2\%}ἐν Πνεύματι Ἁγίῳ.
\par{}\versebeg{1}{9}Καὶ ἐγένετο ἐν ἐκείναις ταῖς ἡμέραις, ἦλθεν \cnote{1:9}{ ιησους~¦~ο ιησους ANT PCK}Ἰησοῦς ἀπὸ \cnote{1:9}{ ναζαρετ~¦~ναζαρεθ SCR}Ναζαρὲτ τῆς Γαλιλαίας, καὶ ἐβαπτίσθη \cnote{1:9}{ υπο ιωαννου εις τον ιορδανην~¦~εις τον ιορδανην υπο ιωαννου ECM\textsuperscript{†} NA SBL TH~¦~εις τον ιορδανην υπο ιωανου WH}ὑπὸ Ἰωάννου εἰς τὸν Ἰορδάνην. 
\versebeg{1}{10}Καὶ \cnote{1:10}{ ευθεως~¦~ευθυς CT}εὐθέως ἀναβαίνων \cnote{1:10}{ απο~¦~εκ CT}ἀπὸ τοῦ ὕδατος, εἶδε σχιζομένους τοὺς οὐρανούς, καὶ τὸ πνεῦμα \cnote{1:10}{ ωσει~¦~ως ANT BYZ CT}ὡσεὶ περιστερὰν καταβαῖνον \cnote{1:10}{ επ~¦~εις ECM\textsuperscript{†} NA SBL TH WH}ἐπ᾿ αὐτόν· 
\versebeg{1}{11}καὶ φωνὴ ἐγένετο ἐκ τῶν οὐρανῶν, Σὺ εἶ ὁ υἱός μου ὁ ἀγαπητός, ἐν \cnote{1:11}{ ω~¦~σοι ANT CT}ᾧ \cnote{1:11}{ ευδοκησα~¦~ηυδοκησα ANT}εὐδόκησα.
\par{}\versebeg{1}{12}Καὶ \cnote{1:12}{ ευθυς~¦~ευθεως ANT PCK}εὐθὺς τὸ πνεῦμα αὐτὸν ἐκβάλλει εἰς τὴν ἔρημον. 
\versebeg{1}{13}Καὶ ἦν \cnote{1:13}{ εκει~¦~\dashes{} CT}ἐκεῖ ἐν τῇ ἐρήμῳ \cnote{1:13}{ ημερας τεσσαρακοντα~¦~τεσσερακοντα ημερας ECM\textsuperscript{†} NA SBL TH WH~¦~ημερας τεσσερακοντα ECM*}ἡμέρας τεσσαράκοντα πειραζόμενος ὑπὸ τοῦ Σατανᾶ, καὶ ἦν μετὰ τῶν θηρίων, καὶ οἱ ἄγγελοι διηκόνουν αὐτῷ.
\par{}\versebeg{1}{14}\cnote{1:14}{ μετα δε 99.2\%~¦~και μετα SBL WH 0.3\%}Μετὰ δὲ τὸ παραδοθῆναι \cnote{1:14}{ τον~¦~\dashes{} ANT}τὸν \cnote{1:14}{ ιωαννην~¦~ιωανην WH}Ἰωάννην, ἦλθεν ὁ Ἰησοῦς εἰς τὴν Γαλιλαίαν, κηρύσσων τὸ εὐαγγέλιον \cnote{1:14}{ της βασιλειας 95.5\%~¦~\dashes{} CT 2.1\%}τῆς βασιλείας τοῦ Θεοῦ, 
\versebeg{1}{15}καὶ λέγων ὅτι Πεπλήρωται ὁ καιρός, καὶ ἤγγικεν ἡ βασιλεία τοῦ Θεοῦ· μετανοεῖτε, καὶ πιστεύετε ἐν τῷ εὐαγγελίῳ.
\par{}\versebeg{1}{16}\cnote{1:16}{ περιπατων δε~¦~και παραγων CT}Περιπατῶν δὲ παρὰ τὴν θάλασσαν τῆς Γαλιλαίας εἶδε Σίμωνα καὶ Ἀνδρέαν τὸν ἀδελφὸν \cnote{1:16}{ αυτου του σιμωνος~¦~αυτου TR~¦~σιμωνος CT}αὐτοῦ τοῦ Σίμωνος \cnote{1:16}{ βαλλοντας αμφιβληστρον 82.8\%~¦~αμφιβαλλοντας CT 0.3\%}βάλλοντας ἀμφίβληστρον ἐν τῇ θαλάσσῃ· ἦσαν γὰρ \cnote{1:16}{ αλιεις~¦~αλεεις TH WH}ἁλιεῖς. 
\versebeg{1}{17}Καὶ εἶπεν αὐτοῖς ὁ Ἰησοῦς, Δεῦτε ὀπίσω μου, καὶ ποιήσω ὑμᾶς γενέσθαι \cnote{1:17}{ αλιεις~¦~αλεεις TH WH}ἁλιεῖς ἀνθρώπων. 
\versebeg{1}{18}Καὶ \cnote{1:18}{ ευθεως~¦~ευθυς CT}εὐθέως ἀφέντες τὰ δίκτυα \cnote{1:18}{ αυτων~¦~\dashes{} CT}αὐτῶν, ἠκολούθησαν αὐτῷ. 
\versebeg{1}{19}Καὶ προβὰς \cnote{1:19}{ εκειθεν~¦~\dashes{} CT}ἐκεῖθεν ὀλίγον, εἶδεν Ἰάκωβον τὸν τοῦ Ζεβεδαίου, καὶ \cnote{1:19}{ ιωαννην~¦~ιωανην WH}Ἰωάννην τὸν ἀδελφὸν αὐτοῦ, καὶ αὐτοὺς ἐν τῷ πλοίῳ καταρτίζοντας τὰ δίκτυα. 
\versebeg{1}{20}Καὶ \cnote{1:20}{ ευθεως~¦~ευθυς CT}εὐθέως ἐκάλεσεν αὐτούς· καὶ ἀφέντες τὸν πατέρα αὐτῶν Ζεβεδαῖον ἐν τῷ πλοίῳ μετὰ τῶν μισθωτῶν ἀπῆλθον ὀπίσω αὐτοῦ.
\par{}\versebeg{1}{21}Καὶ εἰσπορεύονται εἰς \cnote{1:21}{ καπερναουμ~¦~καφαρναουμ CT}Καπερναούμ· καὶ \cnote{1:21}{ ευθεως~¦~ευθυς CT}εὐθέως τοῖς σάββασιν \cnote{1:21}{ εισελθων 97.7\%~¦~\dashes{} SBL 1\%}εἰσελθὼν \cnote{1:21}{ εις την συναγωγην εδιδασκε 97.7\%~¦~εδιδασκεν εις την συναγωγην SBL 0.9\%}εἰς τὴν συναγωγήν, ἐδίδασκε. 
\versebeg{1}{22}Καὶ ἐξεπλήσσοντο ἐπὶ τῇ διδαχῇ αὐτοῦ· ἦν γὰρ διδάσκων αὐτοὺς ὡς ἐξουσίαν ἔχων, καὶ οὐχ ὡς οἱ γραμματεῖς. 
\versebeg{1}{23}\cnote{1:23}{ και~¦~και ευθυς CT}Καὶ ἦν ἐν τῇ συναγωγῇ αὐτῶν ἄνθρωπος ἐν πνεύματι ἀκαθάρτῳ, καὶ ἀνέκραξε, 
\versebeg{1}{24}λέγων, \cnote{1:24}{ εα~¦~\dashes{} ECM\textsuperscript{†} NA SBL TH WH}Ἔα, τί ἡμῖν καὶ σοί, Ἰησοῦ Ναζαρηνέ; Ἦλθες ἀπολέσαι ἡμᾶς; Οἶδά σε τίς εἶ, ὁ ἅγιος τοῦ Θεοῦ. 
\versebeg{1}{25}Καὶ ἐπετίμησεν αὐτῷ ὁ Ἰησοῦς, λέγων, Φιμώθητι, καὶ ἔξελθε ἐξ αὐτοῦ. 
\versebeg{1}{26}Καὶ σπαράξαν αὐτὸν τὸ πνεῦμα τὸ ἀκάθαρτον καὶ \cnote{1:26}{ κραξαν~¦~φωνησαν CT}κράξαν φωνῇ μεγάλῃ, ἐξῆλθεν ἐξ αὐτοῦ. 
\versebeg{1}{27}Καὶ ἐθαμβήθησαν \cnote{1:27}{ παντες~¦~απαντες ECM\textsuperscript{†} NA SBL TH WH}πάντες, ὥστε \cnote{1:27}{ συζητειν~¦~συνζητειν TH WH}συζητεῖν \cnote{1:27}{ πρὸς ἑαυτοὺς 76.4\%~¦~πρὸς αὐτοὺς TR 2\%~¦~αὐτοὺς WH 0.2\%}πρὸς ἑαυτούς, λέγοντας, Τί ἐστι τοῦτο; \cnote{1:27}{ τις η διδαχη η καινη αυτη οτι~¦~διδαχη καινη CT}Τίς ἡ διδαχὴ ἡ καινὴ αὕτη, ὅτι κατ᾿ ἐξουσίαν καὶ τοῖς πνεύμασι τοῖς ἀκαθάρτοις ἐπιτάσσει, καὶ ὑπακούουσιν αὐτῷ; 

\end{document}

Sorry for the length of the code, but I wanted to include everything necessary to demonstrate the effect I'm asking about.

Answer 1

adding

\showoutput
\showboxdepth3

You will see

.
.
.
...\rule(0.4+0.0)x325.21501 % footnote rule
...\kern 2.6
...\hbox(12.04506+3.30003)x325.21501, glue set - 0.52602 []
...\penalty 10000
...\glue(\lineskip) 1.0 % lines too tall
...\hbox(7.99223+3.30003)x325.21501, glue set - 0.55798 []
...\glue(\lineskip) 1.  % lines too tall
...\hbox(7.9893+3.30003)x325.21501, glue set - 0.7947 []
...\glue(\lineskip) 1.0  % lines too tall
...\hbox(7.93364+3.30003)x325.21501, glue set - 0.57613 []
...\glue(\baselineskip) 0.0 % lines _just_ fitted 11pt spacing
...\hbox(7.69997+3.30003)x325.21501, glue set 0.79617 []

so...

if you add

\makeatletter
\DeclareRobustCommand\footnotesize{%
%   \@setfontsize\footnotesize\@ixpt{11}% copied from size11.clo
   \@setfontsize\footnotesize\@ixpt{12}%
   \abovedisplayskip 8\p@ \@plus2\p@ \@minus4\p@
   \abovedisplayshortskip \z@ \@plus\p@
   \belowdisplayshortskip 4\p@ \@plus2\p@ \@minus2\p@
   \def\@listi{\leftmargin\leftmargini
               \topsep 4\p@ \@plus2\p@ \@minus2\p@
               \parsep 2\p@ \@plus\p@ \@minus\p@
               \itemsep \parsep}%
   \belowdisplayskip \abovedisplayskip
}
\makeatother

You get

...\rule(0.4+0.0)x325.21501
...\kern 2.6
...\hbox(12.04506+3.60004)x325.21501, glue set - 0.16206 []
...\penalty 10000
...\glue(\baselineskip) 0.46632
...\hbox(7.93364+1.94237)x325.21501, glue set - 0.47307 []
...\glue(\baselineskip) 1.65767
...\hbox(8.39996+3.60004)x325.21501, glue set - 0.42194 []
...\glue(\baselineskip) 0.0
...\hbox(8.39996+3.60004)x325.21501, glue set - 0.49779 []
...\glue(\baselineskip) 0.0

with even baselines, but spaced out

Or you could be braver and insist on 11pt

\makeatletter
\DeclareRobustCommand\footnotesize{%
%   \@setfontsize\footnotesize\@ixpt{11}% copied from size11.clo
   \@setfontsize\footnotesize\@ixpt{11}%
   \lineskiplimit=-\maxdimen % never use \lineskip
   \let\lineskiplimit\dimen@ % prevent it being reset
   \abovedisplayskip 8\p@ \@plus2\p@ \@minus4\p@
   \abovedisplayshortskip \z@ \@plus\p@
   \belowdisplayshortskip 4\p@ \@plus2\p@ \@minus2\p@
   \def\@listi{\leftmargin\leftmargini
               \topsep 4\p@ \@plus2\p@ \@minus2\p@
               \parsep 2\p@ \@plus\p@ \@minus\p@
               \itemsep \parsep}%
   \belowdisplayskip \abovedisplayskip
}
\makeatother

Producing 11pt spacing even if negative space has to be added

...\rule(0.4+0.0)x325.21501
...\kern 2.6
...\hbox(12.04506+3.30003)x325.21501, glue set - 0.65416 []
...\penalty 10000
...\glue(\baselineskip) -0.23367
...\hbox(7.93364+3.30003)x325.21501, glue set - 0.66957 []
...\glue(\baselineskip) -0.28934
...\hbox(7.9893+3.30003)x325.21501, glue set - 0.86386 []
...\glue(\baselineskip) -0.28934
...\hbox(7.9893+3.30003)x325.21501, glue set - 0.44986 []
...\glue(\baselineskip) -0.28348
...\hbox(7.98344+3.30003)x325.21501, glue set 0.85815 []
...\glue(\baselineskip) -0.28934

You could of course take a middle way and increase the baseline slightly while still suppressing \lineskip