Alright, so far the current design system strikes me this way: the required minimum space between rooms represents the internal/structural bulkhead spaces.
So, with that in mind, I suggest perhaps either a research option (once that system is implemented) to allow rooms to touch, or perhaps add a bulkhead object/"room" while adding a requirement to most/all rooms to have at least one side completely in contact with bulkheads/outer hull. Perhaps both. Or maybe just certain rooms, like let's say anything in the "Storage" category.
My reasoning behind allowing rooms to touch, is that it is quite possible to have a larger internal compartment, that houses multiple systems. At least in modern naval ship design. There may be considerations I haven't factored in, regarding hull/structural integrity in a space faring vessel.
Balancing space saving vs other factors, I would also suggest that rooms that contact others without doors, get less than total HP value, based on how many rooms share that same "bulkhead space." Also, keep in mind that if multiple rooms were directly connected, they would be much harder to secure during hostile boarding operations, or during damage control. So on one hand, you've got more viable internal space, at the cost of higher risks in hazard situations. A fire or hull breach could render critical spaces totally unreachable, or kill most of the crew, thus leading to further problems.
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