The main reason I know that GNOME doesn't implement xdg-decoration is to specifically not have to draw anything itself ontop of the surfaces of clients. It would then need to kinda synchronize the rendering of its stuff with the update loop of the application.

The only time I can remember when Mutter/gnome-shell draws over the client is when it stops updating over the wayland socket (freezes), so there isn't really an update loop it needs to synchronize to.