I'm not sure of the question: auxiliary systems, as noted in the rulebook, have no direct impact on the game. They are meant to simulate "meta" systems, and as such, only become useful or important in campaigns. At the moment there are no official rules for them, which means 100 SUs of "repair" space may mean something completely different in your campaign than in someone else's.
So, I cannot tell what you mean when you say "combinations that seemed reasonable [but don't] seem to work."
Further, if you want to add "hangar" space as an auxiliary system, go right ahead! Find a number that works for you and go with it.
Daniel Kast
Majestic Twelve Games
cricket@mj12games.com