Not only some window managers try to put a newly mapped window
inside the screen, GNUstep also tries to do the same thing
if menu is partially outside the screen.
But when a taskbar exists, there is a XWindow hints to tell
window manager not to put a newly mapped window on top
of the taskbar. Therefore, the virtual screen area
is smaller than the physical one. GNUstep does not
handle this hint and it is not practical to do that
because it is indeed the job of window manager.
So it is a communication problem in my own
opinions between window manager and GNUstep. A fix needs to
see what kind of information a window manager provides
when it placesa a newly mapped window different
than this window originally want to be.

I usually try some other window managers to see whether it is
a bug in GNUstep or not.
On Gnome, you can use openbox3 to replace the default window
manager by 'openbox3 --replace &',
or you can try Azalea, which is a port of openbox3 and handle
GNUstep better `openap Azalea.app --replace &`.

It depends on how window manager place a newly mapped window.
Most window managers won't allow a newly mapped window outside
the screen, therefore, the menu/popup is shifted by window manager.

I have no fix for that, just know the reason.