The application needs to speak a protocol to be able to use it. If you use a X wm your apps need to be able to talk X’s protocol to work, if you use a Wayland compositor your apps need to be able to talk Wayland’s protocol (or run on Xwayland, which is basically an X server that runs inside Wayland).
The wm/compositor abstractions only work if your apps know how to use them via the correct protocol