Users of Russian, Greek, Arabic, Japanese want to be able to type accels using a qwerty layout. Users of French, German, and latin languages do not want it.
Currently the first behaviour is implemented as a gtk+ hack - http://bugzilla.gnome.org/show_bug.cgi?id=162726 . The second set of users suffers.
This behaviour should be implemented in xkb in a configurable way, so that it can be removed from gtk+ and both sets of users can be happy.
xkeyboard-config has nothing to do with it. neither xorg. The apps/toolkits get notifications about both keycodes and keysyms (and modifiers and groups etc). The rest is up to them. If some key produces letter S with group 1, and some other key produces letter S with group 2 - xkb can do nothing with the app looking for the symbol S but not for the keycodes.
AFAIK gtk does not do any bad hacks - it correctly(!) just looks through all the symbols in all groups of the pressed key.
PS Though, being Russian, I personally really like the way gtk behaves - and sincerely cannot understand users having several latin layouts in one configuration