I think you underestimate the flexibility of RetroFE.
There's several ways to tackle this:
1. You put everything in one collection, and add a launcher conf file for the games you want to use a different launcher for. With a few script lines that can be generated automatically.
2. You separate everything in separate collections, and just add a .sub file for one collection in the other. That way all files are pulled in from the other collection, and use that collection's launcher as well.
3. Same as 2, but you keep all files in one collection, simply set the paths for the media and roms to that collection from the other collection, and use an include.txt file to select the files for each collection.
As a simple example of 2, my MSX setup (reduced for the example):
collection msx_cart, containing
Gradius
Gradius 2
Gradius 3
Salamander
collection msx_disk, containing
Undeadline
Aleste 2
SD Snatcher
collection MSX, containing
msx_cart.sub (empty file; this will pull in all games from the msx_cart collection)
msx_disk.sub (empty file; this will pull in all games from the msx_disk collection)
msx_cart and msx_disk each have their own launcher, and by pulling them into the collection MSX, I get one collection containing games from both. As an alternative, I could also have put msx_cart.sub in the msx_disk collection; RetroFE allows mixtures of rom files and .sub files (and even menu.txt) in the same collection.
