I think there should be a new type of "door" called a bulkhead. unlike normal doors it would be its own part/unit in a 2 by 1 or 1 by 1 area.
How it would work:
1) the job of the bulkhead would be to compartmentalize so it can be done without the need to separate your ship using structures or armor by having it so the crew AI will not go through them unless they absolutely have to (like no storage or reactor on their side of the bulkhead)
2) it would cost slightly more than armor but be less resilient
3) if your gonna add boarding you could use the bulkheads as an outside door an have boarders jump from ship to ship.
