The nucleus of an Overline atom is typeset in cramped style. You get the same height of the prime in the denominator of a fraction:
```
\documentclass{article}
\begin{document}
\[
\frac{x'}{x'}
\]
\end{document}
```

[![fraction][1]][1]

You can see that the height of the prime in the denominator is the same as in `\overline{x'}`.

Normally this is desired, but your case requires remedy: use `\cramped` for the first `x'`, but I also suggest adding `\,`.

```
\documentclass[twocolumn]{article}
\usepackage{mathtools} % for amsmath and \cramped

\begin{document}

Without \verb|\cramped|
\[
f(x',\overline{x'})
\]

With \verb|\cramped|
\[
f(\cramped{x'},\overline{x'})
\]

With \verb|\cramped| and \verb|\,|
\[
f(\cramped{x'},\overline{x'}\,)
\]

\end{document}
```
(I use `twocolumn` just to reduce the size of the picture)

[![output][2]][2]

You might force uncramped style by declaring `\displaystyle`
```
f(x',\overline{\displaystyle x'}\,)
```
[![uncramped][3]][3]

Not what I'd like to see, to be honest.


  [1]: https://i.sstatic.net/Z4jRUxfm.png
  [2]: https://i.sstatic.net/trHMa0ay.png
  [3]: https://i.sstatic.net/BHNp9FQz.png