1. How to thread the needle on this one?
2. It's a reason I insist that the Confederation Navy is keen on homogenization of spacecraft and spacecraft components.
3. If you think hangar space is an issue, consider launch tubes.
4. Anyway, consider that a collection of connected hangars are larger than the sum of their parts.
5. The larger space allows spacecraft of various sizes and configurations to be manipulated around like a jigsaw puzzle until the bits sticking out find free space.
6. Ignoring hatches and elevators.
7. One reason we deliberately ignore the issue is because space is at a premium onboard our spacecraft.
8. Optionally, if we have fuel/cargo bays, we can also have hangar/hangar bays, and shift the bulkheads, or walls, around, to fit in odd shaped spacecraft.
9. If there's some reason you need bulkheads to wall off individual spacecraft.