Like this?

- Rules defined in
booktabs
package has small gape above and below rule, consequently the are not intended for table with vertical lines.
- It is not clear, why your table you use the
threeparttable
when you not use any its features.
- I would not use
scalebox
, better is use table environment for example as is tabularx
where you can prescribe table width. With use its X
column type the text in cells in such column is automatic break into more lines (well, this you can obtain with p{<width>}
columns too).
- Instead of switch from
\twocolumn
document to \onecolumn
(and than back again) is better to use table*
float environment. Using it, table will appear on the top of the next page from where is inserted in the text.
\documentclass[final,5p,twocolumn]{elsarticle}
\usepackage{float, enumitem, amsmath}
\usepackage{rotating} % new
\usepackage{booktabs, makecell, multirow, tabularx, threeparttable}
\renewcommand\theadfont{\small\bfseries}
\renewcommand\theadgape{} % new
\usepackage[table]{xcolor}% changed, instead of color, colortbl
%\usepackage{adjustbox} % not used in this MWE
%\usepackage{todonotes} % not used in this MWE
\usepackage{caption}
\captionsetup{belowskip=-5pt}
\captionsetup[table]{justification=raggedright,singlelinecheck=off}
%\usepackage{subcaption} % not used in this MWE
\begin{document}
\begin{table*}
\centering
\settowidth\rotheadsize{\theadfont Description 3 }
\renewcommand\arraystretch{1.1}
\caption{Simple caption.}
\label{tab:setTag}
%\begin{adjustbox}{width=0.9\textwidth,center=\textwidth}
%\begin{threeparttable}
\begin{tabularx}{\linewidth}{l | l *{2}{>{\centering\arraybackslash}X}}
\Xhline{1pt}
& \thead[l]{Results}
& \thead{Method 1} & \thead{Method 2} \\
\Xhline{0.7pt}
& & \multicolumn{2}{c}{First section} \\
\Xcline{3-4}{0.6pt}
\multirow{16}{*}{\rothead{Description 1}}
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\ \Xcline{3-4}{0.6pt}
& & \multicolumn{2}{c}{Second section} \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\ \Xcline{3-4}{0.6pt}
& & \multicolumn{2}{c}{Third section} \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\ \Xcline{3-4}{0.7pt}
\rowcolor{gray!10}
& & \multicolumn{2}{c}{First section} \\
\rowcolor{gray!10}
& Very long name & Something pretty long too & Something else even longer than before \\ \Xcline{3-4}{0.7pt}
\rowcolor{gray!10}
& &\multicolumn{2}{c}{Second section} \\
\Xcline{3-4}{0.7pt}
\rowcolor{gray!10}
& Very long name & Something pretty long too & Something else even longer than before \\
\rowcolor{gray!10}
& Very long name & Something pretty long too & Something else even longer than before \\ \Xcline{3-4}{0.7pt}
\rowcolor{gray!10}
& &\multicolumn{2}{c}{Third section} \\
\Xcline{3-4}{0.6pt}
\rowcolor{gray!10}
& Very long name & Something pretty long too & Something else even longer than before \\
\rowcolor{gray!10}
\multirow{-8}{*}{\rothead{Description 2}}
& Very long name & Something pretty long too & Something else even longer than before \\
% \Xcline{3-4}{0.7pt}
% & &\multicolumn{2}{c}{First section} \\
% \Xcline{3-4}{0.7pt}
%\multirow{1}{*}{\rotatebox[origin=c]{90}{~Description 3}}
% & Very long name & Something pretty long too & Something else even longer than before \\
% \Xcline{3-4}{0.7pt}
\Xhline{1pt}
\end{tabularx}
%\end{threeparttable}
%\end{adjustbox}
\end{table*}
\end{document}
Addendum:
A possible solution or third part of table, where instead of "Description 3" in the first column is used abbreviation "D. 3". Association to their meaning is given with "Description 1 (D. 1)" and "Description 2 (D. 2)" in the first two parts of table.
\documentclass[final,5p,twocolumn]{elsarticle}
\usepackage{float, enumitem, amsmath}
\usepackage{rotating}
\usepackage{booktabs, makecell, multirow, tabularx, threeparttable}
\renewcommand\theadfont{\small\bfseries}
\renewcommand\theadgape{}
\usepackage[table]{xcolor}
\usepackage{caption}
\captionsetup{belowskip=-5pt}
\captionsetup[table]{justification=raggedright,singlelinecheck=off}
\usepackage{subcaption}
\begin{document}
\begin{table*}
\centering
\settowidth\rotheadsize{\theadfont Description 3 (D. 3)}
\renewcommand\arraystretch{1.1}
\caption{Simple caption.}
\label{tab:setTag}
\begin{tabularx}{\linewidth}{l | l *{2}{>{\centering\arraybackslash}X}}
\Xhline{1pt}
& \thead[l]{Results}
& \thead{Method 1} & \thead{Method 2} \\
\Xhline{0.7pt}
& & \multicolumn{2}{c}{First section} \\
\Xcline{3-4}{0.6pt}
\multirow{16}{*}{\rothead{Description 1 (D.\,1)}}
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\ \Xcline{3-4}{0.6pt}
& & \multicolumn{2}{c}{Second section} \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\ \Xcline{3-4}{0.6pt}
& & \multicolumn{2}{c}{Third section} \\
& Very long name & Something pretty long too & Something else even longer than before \\
& Very long name & Something pretty long too & Something else even longer than before \\
\Xcline{3-4}{0.7pt}
\rowcolor{gray!10}
& & \multicolumn{2}{c}{First section} \\
\rowcolor{gray!10}
& Very long name & Something pretty long too & Something else even longer than before \\ \Xcline{3-4}{0.8pt}
\rowcolor{gray!10}
& &\multicolumn{2}{c}{Second section} \\
\rowcolor{gray!10}
& Very long name & Something pretty long too & Something else even longer than before \\
\rowcolor{gray!10}
& Very long name & Something pretty long too & Something else even longer than before \\ \Xcline{3-4}{0.8pt}
\rowcolor{gray!10}
& &\multicolumn{2}{c}{Third section} \\
\rowcolor{gray!10}
& Very long name & Something pretty long too & Something else even longer than before \\
\rowcolor{gray!10}
\multirow{-8}{*}{\rothead{Description 2 (D.\,2)}}
& Very long name & Something pretty long too & Something else even longer than before \\
\Xcline{3-4}{0.6pt}
\settowidth\rotheadsize{\theadfont(D.\,3)} % <--- changed (reduced) \rothead size
\multirow{2}{*}{\rothead{(D.\,3)}}
& &\multicolumn{2}{c}{First section} \\
& Very long name & Something pretty long too & Something else even longer than before \\[1.5ex]
\Xhline{1pt}
\end{tabularx}
\end{table*}
\end{document}
