I agree that wm-stackorder-5.2 (and wm-stackorder-6.1) should be flagged as
inappropriate for Aqua.  As far as I can tell, the stacking restrictions
that they are checking for are:
* not required by the language specification
* not useful in the typical applications of overrideredirect windows
* not natural in the context of Apple's window manager (because *all* NSWindows
  appear in the stacking order and can be reordered)
* implementable at the script level if really needed.

I suspect that this is just a quirky behavior of some X11 window managers which
some people came to expect, but which is mostly irrelevant to applications.

I am going to commit this change to the bugfix branch, before I forget about it.
We can revisit it before merging, if something comes up.