I have also been trying to make sense in my head about where on these ships the various rooms have come from.
Am I getting the wrong end of the stick and thinking that the station is made up of whole ships smushed together? When really other ships were just pulled apart to construct the station?

(sorry for crappy paint skills)
Oh, and another thought, as it is multiple ships smushed together, there should be multiple teleport locations as each ship would have had its own teleporter.
That could be used to easily get from one section to another for players who don't want to run and jump their way across the whole station to get to somewhere.