Something like this could probably be versatile/adaptable enough to accommodate - a living quarters with terminals and equipment rack, a flexible cargo bay room with SRV / Fighter bay / Dropship hangar (or better if the function of dropship could do just regular cargo bay without any extra modules) that changes it's layout and available vehicles for interaction depending on modules fitted, a PP room, and 1-3 (depends on ship size and slots size/possible modules) extra rooms for other modules with possible gameplay / minigames. It could be enough space to put gameplay in and varied enough to give the feeling of actual interior for immersion.
I don't think we need to access actual cargo holds, or refineries, or controllers, etc. Cargo holds maybe someday way into the future, if there are ways to load them and a possibility for at least some form of extended contraband gameplay, but for initial implementation - no need.
Passengers are probably out of the realm of possibility, simply because it is possible to have a lot of them on some ships and to place and render that much would probably be hard. As much as I would love passengers gameplay, but without severe cut downs I don't think it's realistic. Maybe there could be only a limited number of interactable NPCs in a separate room (leaders of groups or something like that) with other passengers not visible, plus VIP/First class. But that also could be something for the future additions with specific gameplay for them.
Something like that I would love to have. Could seal the rooms to make oxygen reserves last longer. Possibility to vent an atmosphere in specific rooms/sections for 'some' purposes. Yep, if there is a framework for something like that - the gameplay can follow.
If for everything to be completely seamless, without faking anything - yes. But if there are some fakery involved, hidden loading screens behind animations, decreases and increases of details, etc - no overhauls are needed, Game Engine can do it, obviously it would require not a simple development process and quite a creative approach to designing this fakery to be subtle enough, but I think it could be done to be perceived as seamless without much disruption to the process of movement and play.
On that I can only say - Very Yes to limpets size/mass, never made sense to me, apart from - ok, they are of a similar volume so for the sake of simplicity we are going to count them as the same mass because that is how cargo holds are working in the game. Would be nice if that was looked at again, maybe make cargo in volume units and only items/commodities that have ~1 ton mass add to ship mass, or something like that. But apart from that - I'm not really qualified to talk about cargo, as hauling is very mind numbing to me and no amount of extra static details could change that, haha.