How to stop Gnome from overriding XKB layout
Solution 1:
It is was same as Unity in version 1 of settings daemon, now it is changed with Gnome (version 3 of settings daemon)
Sometimes, I think developers are just fighting user who don't want changes or need low level customization. Gnome is now creates layers.
Just move /usr/lib/gnome-settings-daemon/gsd-keyboard somewhere else to disable it. gnome-settings-daemon need to be restarted or just reboot.