Conflict between microtype, LuaLaTeX, and otf fonts when typesetting material in small-caps

Question

I'm using the microtype package (microtype beta 2.5 build 08) to modify my document and I'd like to retain its functionality across all font shapes with the exception of small-caps (\scshape). How do I do this?

I'm asking this because microtype is not preserving the (\scshape) of section names listed in my table of contents whenever I use otf fonts (adobe caslon pro, adobe garamond pro, etc) that are loaded via fontspec. Instead, it's changing them to regular text. Whenever I don't load micro type, the text reverts to scshape. I'd like to keep the (\scshape) of the section names intact while using microtype without having to abandon use of the aforementioned otf fonts.

Here is what my toc looks like when microtype is enabled:

Here it is with microtype disabled:

I'm building my documents with Lualatex to facilitate loading of otf fonts and their usage with microtype. I notice this issue doesn't occur when using normal latex fonts.

Here is my code:

\documentclass[dotinlabels,nohyper]{tufte-book}
\usepackage{amsthm}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{fontspec}
\setmainfont[Ligatures=TeX]{Minion Pro}
\usepackage{fancyhdr}
\pagestyle{fancy}
\usepackage[unicode=true,
 bookmarks=true,bookmarksnumbered=true,bookmarksopen=false,
 breaklinks=false,pdfborder={0 0 1},backref=false,colorlinks=true]
 {hyperref}
\usepackage{titletoc}
\usepackage{titlesec}
\usepackage{tocloft}
% If you do not load micro type below, small caps are preserved.
\usepackage[activate={true,nocompatibility},final,tracking=true,factor=1100,stretch=10,shrink=0]{microtype} 

\hypersetup{linktocpage=true}

\setcounter{secnumdepth}{1}

\setcounter{tocdepth}{2}

%formatting for toc entries
\renewcommand{\cftsecfont}{\large\scshape\MakeLowercase} 
\renewcommand{\cfttoctitlefont}{\scshape\MakeUppercase}
\renewcommand{\cftsecdotsep}{\cftdotsep}
\renewcommand{\cftsecpagefont}{\scshape}
%

\titleformat{\section}{\titlerule\vspace{.8ex}%
\Large\bfseries}{\Large\thesection.}{.5em}{}

\renewcommand{\sectionmark}[1]{%
  \markboth{}{\thesection.\ #1}}

\newcommand{\hsp}{\hspace{20pt}}

%Chapter title Formatting
\definecolor{gray75}{gray}{0.75}
\titlespacing{\chapter}{0pt}{*0}{*5}
\titleformat{\chapter}[hang]{\Huge\bfseries}{\thechapter\hsp\textcolor{gray75}{|}\hsp}{0pt}{\huge\bfseries}
%

\begin{document}
\fancyhf{} % clear all header/footer fields 
\fancyhead[RO]{\scshape\normalsize\MakeLowercase{\rightmark}} 
\fancyfoot[R]{\thepage} 

\tableofcontents{}

\chapter{Preliminaries}
\section{Mathematical Induction}
text goes here...
\newpage{}
test
\newpage{}
test
\end{document}

Answer 1

The reason why the small caps font is changed to the regular one is that microtype's tracking feature does not work flawlessly with lualatex. At the moment, the only fix (apart from not using tracking altogether) is to load the font with Renderer=Basic instead of (the default) Full:

\setmainfont[Ligatures=TeX,Renderer=Basic]{Minion Pro}

Unfortunately, this may have side effects, as switching to the basic renderer means losing some OpenType features. In the case of small caps, for example, less kerning pairs will be defined. While more problems may still be uncovered, there is also the one or the other bug with Renderer=Full.

---

[I was going to suggest to restrict this to the small caps font:

\setmainfont[Ligatures=TeX,SmallCapsFeatures={Renderer=Basic}]{Minion Pro}

but this does not work.]

Answer 2

The microtype package offers to define sets of fonts. There is even a pre-defined set name called smallcaps, though it is not of much use as one can apparently only include sets for activated micro-typography.

Excluding small caps would be the same like including everything else.

Code

\documentclass{article}
\usepackage[
    protrusion=false,
    expansion=false,
]{microtype}
\DeclareMicrotypeSet{non Small Caps}{shape={it*,up*,sl*}}
\microtypesetup{activate=non Small Caps}
\usepackage{lipsum}
\begin{document}
{\scshape\lipsum}
{\itshape\lipsum}
\end{document}

But as I understand it, this would overwrite every default settings made by microtype; therefore it seems easier to just patch \scshape.

Code

\documentclass{article}
\usepackage{microtype}
\expandafter\def\expandafter\scshape\expandafter{\scshape\microtypesetup{activate=false}}
\usepackage{lipsum}
\begin{document}
{\scshape\lipsum}
{\itshape\lipsum}
\end{document}

Answer 3

I'm not sure which aspects of microtype you wish to disable when it comes to dealing with small-caps fonts. I'll assume that it's the tracking (inter-letter and inter-word spacing) that you want to disable. (Somehow, I don't think you want to disable character protrusion optimization for small-caps glyphs.)

To disable microtype's action with regard to tracking for small-caps characters only, you could issue the following command (after loading the microtype package, obviously):

\SetTracking[spacing = {0,0,0}]{encoding=*,shape=sc}{0}