What you're trying to do probably isn't supported with roadblst and some of its clones. It's not a mode that QMC2 has or will ever export sets, so I'm out of here...
Well fully merged sets are very standard and are perfectly supported by QMC2 except for this edge case.
But yeah, as you're using the MAME internal rom checker to check the roms, it's not really a QMC2 thing.
The more i think about it, the more i am sure that the only workaround would be to use the "Space-efficient" way.
But that means that the other way is no more feasible (there was no problem until this set).