@Riverstorm discussions are good! all i'm saying is that it would take a non-trivial code change to get the lr-mame2003 core (and retroarch) to cope with letting the user control loading individual games from a merged set.
here's the best idea i can come up with: something like how lr-fba-next dynamically builds core options around inputs, based the game. it's feasible that you you could dynamically generate a list of clones for each game, and then let the user select, and save it as a unique core option. BUT you'd have to reset the game for the desired clone to loan. this change is possible but for me it's complex, and i don't see huge value in it.
either way, it's retroarch and libretro changes that are required to solve this problem, because all ES can do is send command-line arguments, but retroarch/libretro have to interpret them. that's all i was really trying to say.
i learnt how mame deals with merged sets, so i'm happy! sorry if i'm being negative.. i'd absolutely love for more people to get engaged with making changes. it's fun!