>> So this clearly points to a bug in the way GNOME handles the Emacs 
>> frame. There's one last thing you could try: under GNOME, try the same 
>> experiment, but with Emacs fullscreen.  I've read that GNOME 
>> automatically disables its compositor when an app is fullscreen, but 
>> I'm not 100% sure that's the case.
>
> I am unable to reproduce this with Emacs fullscreen.
>
> But fullscreen mode removes the window chrome, including the titlebar, 
> so that might have something to do with it.
>

I think it's now clear that there is a bug in GNOME.  The main difference 
between running fullscreen and non-fullscreen in this context is that the 
compositor is bypassed.  This is mainly for (fullscreen) games, who have 
direct access to the screen, which is more performant.  If you manage to 
create a MRE without your full config, you could file a bug report and 
point to that difference between fullscreen and non-fullscreen behavior.