Due to different spelling I still have some games without overlays. So I edited the config files manually and found something.
Game: Godzilla - Kaijuu Daikessen (Japan)
Issue: Missing overlay and mixed spelling
Desc: The file is in the config folder of the SNES repo but if you take a look inside it points to the CFG in the SFC overlay folder. The game name spelling is also different (Godzilla/Gojira). The problem is... there is neither in the SNES repo nor in the SFC a Godzilla/Gojira PNG or CFG in the overlay folder.
Game: Assault Suits Valken (Japan)
Issue: Missing overlay
Desc: Same as Godzilla - Kaijuu Daikessen (Japan)
Game: Super Boss Gaiden
Issue: completely missing