Xwayland has a lot of bugs with transparent always-on-top windows. You'll get weird stuff like the 'click''s that are supposed to go through it will in fact go through multiple windows down to the next xwayland app, bypassing whichever native gtk app they should have interacted with.
Damnit, and here I was going to port Clippy to Linux. Found the sprite sheet and everything.
…actually, I was working on putting clippy in blender a long time ago but the way it does (did?) window animations meant the animations would only work while the mouse was actively over the subwindow and (IIRC) was moving.