Happily, Unification I and II are on the same disc and not split the way most two-parters were in the DVD sets.
If they follow their standard 5 5 5 5 4 2 episode format on the discs, Chain of Command will be split across two discs in season 6. I assume they will put 4 episodes on disc one or two to prevent that. They haven't always put the maximum amount of episodes on disc one, so they will probably accommodate that.
Birthright and Gambit will be clean either way.