Default keyboard layout always used for shortcuts in Wayland
Switching between keyboard layouts works correctly for normal text entry, but the layout used for shortcuts is always the default one. This means that if a key is in a different position between the active layout and the default layout, the wrong shortcut is sent for the non-default layouts.
For example, if the default layout is qwerty, then to use ctrl+s as a shortcut I will always have to press the same physical key (button 32 on a usb keyboard) no matter where 's' is in currently active layout.
Changing the default layout in the gnome settings dialogue will immediately change which layout is used for keyboard shortcuts.
This only happens under Wayland, and for all GTK3 apps I have tried it against. Older GTK2 apps don't have this behaviour. Firefox also correctly handles the layout change.
The one exception to this I have found is in gnome-shell where ctrl+alt+t (open new terminal) will function correctly in all layouts.