You can't isolate both battery from the alternator if it has to charge them both. The issue is what does the VR see voltage wise. The fully charger battery would present a high voltage to indicate lower field current. But the charged battery would discharge to charge the low battery until both were at equal voltage. If one battery different from age/use, you would have an imbalance.

Charging multiple batteries requires a smart system. Paralleled batteries and alternators/generators would require a governor system. Otherwise load sharing is not equal.