That's why there was a protocol released to do just that, by having the client set a unique tag when it creates its windows so the display server can recognize

That's why there was a protocol released to do just that, by having the client set a unique tag when it creates its windows so the display server can recognize when a window has come back. Wayland in general is all about leaving stuff up to the display server, with the display server representing the current user and their current window management preferences.