From what I've seen, for individual game, the Bezel Project uses the RetroArch's configuration override feature, by creating an overlay config in /opt/retropie/configs/all/retroarch/<core_name>/<game_name>.cfg (see an example here).
It doesn't overwrite RetroPie's ROM folder configuration (/opt/retropie/config/arcade/retroarch.cfg) or any of the .cfg file in the ROM folders.
So, referring to the 2 configuration examples above, I don't think they'll be impacted. Anyway, take a backup before adding the bezels, just to be safe. Make sure you have enough free space, since the they take quite some space (just the MAME bezels take more than 1Gb).