Well, Geany doesn't know anything about keyboard layouts, it just gets keycodes from GTK and compares them to the value set, and as you can see GTK is delivering different keycodes for the different layouts.
So there is not really anything in Geany to "fix".
I am not sure why ctrl+v continues to work, but the mapping of `v` varies between different Russian layout mappings as I understand, so GTK may be doing something "smart" there.