See, that's how it should/could work in my head.
Systems/Sectors would have a "Main Trade Hub" which'd be where the large ships dock, at which point NPCs or players could distribute cargo between the dock and the other stations in the region.
These "Trade Hubs" would, of course, likely become a hotspot for piracy and "emergent gameplay" so docking a large ship safely might become a Squadron operation, where the large ship would need a combat escort and cargo haulers in order to unload quickly, without incident.