I can make my peace with 3D printing. I know not everyone will, but I can.
But consider some ideas here:
-3D printing is only part of the process. Maybe it doesn't make
everything. Just the bulky easy to assemble stuff like the hull and whatnot. I'm thinking of this more in terms of the proposed hanger bay mechanics for fighters. Maybe when you buy a "kit" it's a matter of having the engines and weapons and whatnot already assembled, but the ship creates hull and whatnot it all goes into. Win win - because it uses up significantly less tech without feeling quite like magic by assembling
everything (including a power source)
-In order to make an exact copy of your ship (engineer mods included) you can't just scan it or upload datapoints - it has to actually be disassembled at a molecular level (3D DEprinted

) to get it exact. Those materials on the starting end are then used in construction of other ships on the station. At your destination station, your licence allows you to receive an exact copy based on that deconstruction, at which point the information is purged. Technically you could make copies, sure, but the bureaucracy of the galaxy and the power that corporations wield pretty much ensures that messing with licences and IP isn't going to happen (a whole station could be shut down over such infractions, etc...)
-The process a ship is reassembled is not unlike how Insurance works, and in fact the money spent probably goes through similar hands. (Bank of Zaonce?) So whatever magic makes insurance profitable for them (because, let's face it, it's NOT by any way we can imagine) is the same mechanic that allows this recycling/transfer mechanic to work. It should be at a premium, I personally believe, though, especially the further you go.
Any of that help?