Looking back at my initial comment, I notice I worded it badly enough for me to wonder how I am the one that wrote it... Sorry about that.
The window_mouse_get_delta_x() and window_mouse_get_delta_y() functions work fine, assuming the mouse would be locked to the center of the window. The issue is window_mouse_set_locked(true) marking the mouse as locked, but not actually locking it. The only functions from this extension which I think I'll need are display_mouse_lock() and maybe display_mouse_unlock().
I also looked up XGrabPointer, but I think that only works on X11. GameMaker's built-in window_mouse_set_locked(true) already has proper support on X11 I think, I need support for Wayland.
If filing a bug report is the best option, then I'll be doing that.