I would hazard a guess that the costs for the various facilities listed in Equipment are when they are in a planet-based environment, whereas the costs in the Spaceships chapter are when they are used as modules aboard spaceship and space stations. If you're using them as ship modules, use the costs under the Spaceship chapter listings.
One might want to restrict the Trauma Lab, given that it makes sense to do so. I am, for my campaign games.
I would say that you can salvage modules and spare parts if the characters' ship has a Salvage Station module. How many spare parts you might get, and whether any modules salvaged are functional is something that I would leave to the GM.
Hope this helps.