Ah, a fellow SSS and GalCiv2 fan?
I would agree with snap points, and of having 'internal slots', since it would make things a little easier.
Another option would be a sort of grid setup, like the old game Outpost. (Mars? Try building on other planets in general)
There are the main structures, and 'tubes', the connecting passages (both strait and + shaped)
Although for MC:C, the connecting passages (like where the med bed/fridge is) is technically a 'tube' in the Outpost sense, since it is as much a connecting passage way as it is an occupied space.
For the airlock issue.
A 'doorway slot' for connecting sections and hub sections. This 'doorway slot' is made up of either a door (or open doorway for connected areas), or an 'end cap/wall section', and an adjacent 'interior slot' on the interior side. The doors would be slightly 'above' the actual 'opening' (so the 'frame' of the door fills the rest of the 'opening'), so they won't 'hit' the floor. The 'interior slot' is 'allocated' to an installed doorway, to make a 'you cannot put stuff here' type of zone. That way if any sort of doorway is in place, items cannot be put there and so won't block the door. If movable objects are there when a doorway/airlock door is set to be installed, the game relocates the item to the nearest empty spot/interior slot (or the closest designated area for putting carried items/equipment, like an equipment rack for example). If fixed equipment takes up the interior slot adjacent to an end cap, the interior module first has to be removed/relocated before a doorway can be installed.
Would that type of thing work?
Another thing to consider.
What all players could be allowed (or want to do) with setting up stuff base sections themselves.
One player might stick with the present setup that has structures with connecting passages. Another might want to focus materials on structures grouped together for optimal internal space (hope nothing bad happens). Yet another might go with a decentralized setup, having two or more sections, each dedicated to certain aspects (hope the life support/power pipes between sections don't get damaged if life support and living spaces are in separate base sections). Another might do something redundant, and use their 'extra' initial allocated stuff to have two separate base sections each with their own life support (which raises its own issues if the ice deposits can only support two pumps, and require an option to operate separators at reduced capacity without shutting down due to limited water supply)
Secondary building locations would also be nice, for optional support structures/equipment. Maybe prototype vertical wind turbines (or extra solar panels) on a hill next to the main base (extra power, handy for an optional challenge, maybe some event or a 'donation' meaning the base is short one or more working RSGs), or a shelter/ELS setup near a major group of mineral deposit that are a fair distance from the base (who want's to go for off road driving in a rover during a storm if a suitable shelter is nearby?).
Maybe an option for multiple level structures? Would 'basements' or 'underground construction' or building partly into a hill be a viable option?
Also... Berths... we need berths. Be they double or triple berths or just single berths/beds. We have a toilet, but where are colonists supposed to sleep? Even if it is more for immersion/realism and not actually used. (Maybe a quick 'nap' to more quickly recharge the stamina bar? Have stamina drain slower but recover a lot slower to require rest to be a needed factor?). Hot bunking with a double berth basically means sleeping space for four. (like maybe placed where the waste containers usually are next to food prep in MC:C 1.x)
I also have other ideas in mind (probably best to hold off since they go beyond just basic base building). One of which is a 'main base' that the players deal with when it comes to requesting stuff to be delivered (like construction teams to build another base segment), and to open up other options/possibilities for missions and such.