I think we’ve got it pinned down for the most part. It seems to be related to some libdecor changes that were added recently to enable window decorations. Historically, the window has just floated in the air in wayland, but the libdecor stuff lets it act like a normal program window.
This PR fixes the 0 B window issue, apparently: https://github.com/libretro/RetroArch/pull/13759