> However, some clones contain identical roms which the parent set also has.

If the parent has the rom (and the mentioned mk file is NOT an example of this), the rebuilder rebuilds the rom ONLY to the parentset if "split merged" is used.


> mkla1.zip and mkla2.zip
>
> both files contain the mkg-u106.rom file which I wouldn't expect to be in both
> sets.


Well..you're wrong. Both sets needs the files since the mentioned rom is not a rom of their parentsets (set: mk). There are several other sets in MAME where you have double roms in clones. That's because of the way the developers chose the parent and the clones.

Roman Scherzer
ClrMamePro