I like to ignore certain aspects of freelancer... hard though it may be with my Literal thinking mind.
I instead try to imagine what the systems, planets and stations would be like in a 'to scale' version of the game/mod...
I'm off to look for an existing thread related to the scale of the game...
One way to look at scale would be to visualise Freeports not as a single large base - but a collection of smaller modules built up over time.
So when you see a base with 4 domes sticking out - try to imagine instead an array of many such modules linked together in all sorts of interesting ways. Newer bases in Disco try to hint at that kind of layout, but after hundreds of 'real' years - the Freeports and other long established bases would be truly massive, sprawling complexes of base modules.
This kind of 'space suburbia' is cheaper to construct than a single massive base (being composed of smaller, transportable prefabs). It would also be safer, because if one small dome goes 'pop' - it is nowhere near as bad as one single large dome getting a hole in it...