[Spaceships] Is This Legal?

[RogerBW]

I think the "a ship one SM smaller as the front six systems of the big ship" approach is not necessarily appropriate for ships where the back section can operate autonomously. For the big plane with a spaceship on top, I'd be more inclined to have six systems of Hangar Bay or even Cargo in the midsection, or just a huge External Clamp (and change performance accordingly for the payload craft).

If you do still want to use the Upper Stage approach, then armouring one of the central systems will be vital for a fly-back booster.