can you try to edit this file :
/recalbox/share_init/system/.emulationstation/es_systems.cfg
then, save the overlay or just rerun es : /etc/init.d/S31emulationstation restart
tell me if that works.
if yes, please do a pr or tell me the modification so that i put it for the next batocera version.
have you tested the c64 on batocera ? i'm not familiar with c64, can you confirm that it works as expected please ?