Why is the fraction off the math axis in XeTeX?
I played a bit ... black is xelatex
and red lualatex
and yes, this is not an answer ...
\documentclass{standalone}
\usepackage{amsmath,xcolor}
\usepackage{unicode-math}
\setmathfont{xits-math.otf}
\begin{document}
\makebox[0pt][l]{\raisebox{-1.6ex}{\includegraphics{xetex}}}%
\textcolor{red}{$-\frac12=-\dfrac12=-\tfrac12$}
\end{document}
This seems to be fixed in the development version of XeTeX (looks like it was the same underlying issue as \setbox containing maths interferes with surrounding math mode in XeTeX):