If they keep that same pattern as season 1 going, the separate parts for Unification, Chain of Command, Birthright will all be together on the same disc. The exception is Gambit, which are the 4th and 5th episodes of the season. I'm sure the guys putting the discs together will notice that, and adjust the disc content accordingly.
Would be cool, if they put both versions, the regular two part episodes and the one part movie versions on the discs. With seamless branching, only a few minutes of credit parts would have to be duplicated.