The following code
% !TEX program = XeLaTeX
\documentclass{article}
\usepackage{unicode-math,mathtools}
\begin{document}
$\overline{A}\overline{A}\mathrlap{A}$
\end{document}
gives
Going deeper
Through some experiments, I found that mathtools and \mathclap are not to blame.
% !TEX program = XeLaTeX
\documentclass{article}
\usepackage{unicode-math}
\begin{document}
$\overline{B}\overline{B}\hbox{$\scriptstyle B$}$
\end{document}
This disagreement is restricted to
- The package
unicode-math - XeLaTeX (LuaLaTeX is fine)
- The first
\overline(The second is fine.\underlineis fine) \hboxcontainingscriptstyleand something printable.
One may also try this
$\overline{C}\overline{C}\mathchoice{}{}{}{\hbox{$\scriptstyle C$}}$
I have no idea how to go deeper. Any idea?



\fontdimens are messed up there. This is basically another incarnation of the problem reported here: Why is the fraction off the math axis in XeTeX?. Use LuaLaTeX instead. – Henri Menke Aug 05 '16 at 16:28