I would like to know this too!
When I imported my Amiga, SNES, NES and MAME games I enabled the download of the "bezels". But there are a few games where these (slightly transparent) bezels cover parts of the game.
So I would like to disable the bezels for these specific games.
I have seen that RetroArch has an "Overlay" setting where I can disable these bezels, however that change does not stick, when I launch the game again then the bezels are there again - saving the config inside of RetroArch while the game is running throws an error that the config cant be saved.
A option to disable bezels entirely or on a game by game basis inside of LaunchBox would be great! (I could not find such an option)