>> This does not happen with M-x toggle-frame-fullscreen RET.
>
> Your scenario is complicated by the fact that the only means I know to
> put Emacs in fullscreen mode is F11.  Does it happen with maximized
> frames too?

No, it only happens in window-manager triggered fullstreen, not in
a maximized frame.

I use i3 as a window manager.  I hope you or somebody else can try
the recipe above and confirm the bug.

>> The attached patch for Org fixes the issue but I guess there
>> is a more general issue here.
>
> Please explain what the "issue" is, how it is related to `org-mode', and
> how it is related to `window-resize-pixelwise'.  The latter is a user
> option and should not be set by an application.

For the issue, see the backtrace.  For the rest, I don't know.

-- 
 Bastien