There are multiple arcade rom folders, you know. You could pretty easily dedicated one to mame2010, and the other to mame2003, for instance some people have the neogeo folder as mame2003 and mame as mame2010.
Alternatively, you could do what I do and just use subfolders. So you would have mame/mame2003plus and mame/mame2010. Then you could just set the specified emulator for each folder. If you need help with the syntax: https://wiki.batocera.org/batocera_conf_syntax
Alternatively duex, you could go into the game options for each game and set it to its appropriate emulator. This is probably what most users would do.
