Yes, you can set a game specific launcher in the launchers directory of a collection, e.g. you want to use the mame64 launcher (in stead of the mame launcher) for daytona in the arcade collection, you'd create a collections\arcade\launchers\daytona.conf file, in which you simply put the single word
mame64
This will use the launchers\mame64.conf launcher in stead of the launchers\mame.conf launcher.
I really should explain this better in the documentation; I still haven't been able to find this feature, even though I programmed it ages ago.