The problem is that the Split and Merged sets have files that aren't actual game roms but are required for certain games to work. Neogeo.zip and Qsound.zip are just 2 examples, these 2 bios files are required for NeoGeo and Capcom CPS2 games to work, there are others as well but that's the main obvious ones.
It is possible to do what you are asking I am sure but it would be an annoying task to do. If you want a pared down set I would suggest getting a Non Merged set and pull individual rom files out of that and build your customized set, I have done this for my No Filler project.