It comes to my mind that with these new 3D (quantum) printers practically all you need to transfer is the complete quantum state of your old ship, which could be done in pretty much an instant, and then have it printed out in the hangar, which would take some time ofc.
Giving it some further thought I may have an explanation why we can have instant ship teleportation but still need hyperspace travel.
Mind you, I'm just trying to wrap my head around the fact of Frontier's instant transfer mechanism and though I'd prefer a more conventional ingame solution, I think we are stuck with it.
So, say there is quantum scanner/3D printer at every Shipyard/Outfitting facility, then the above method would be used to transfer your ship.
Why isn't there every kind of ship available at every shipyard then?
Because ships still have to be manufactured and the quantum teleportation method is only used to move them about.
More particularily, the quantum scanner would extract the quantum state of your ship, which destroys the original ship and leaves behind an entropic cloud of particles only.
This unstructured particle cloud would be claimed by the respecticve transfer organisation to make up for the use of the same amount of particles at the receiving end.
The actual transmission of the extracted quantum state to the 3D quantum printer at the target location is pretty much instantaneously (quantum entanglement) and the ship is fully reprinted after some amount of time.
The license to extract the quantum state of a ship has to be bought from the ship manufacturer. The use of it entails a certain fee depending on the ship model and any misuse is rigidly prosecuted and severely punished.
As ships, though containing quite a large number of particles, are fairly homogenous, one could even imagine the use of some clever 'compression' algorithms to reduce the inforamtion amount and complexity of the transmitted quantum state, thus making the use fairly cheap and quite commonplace in 3302.
These 'compression' algorithms would also safeguard the manufacturer against any piracy, as they are known only to them and any 3rd party meddling with the transfer signal is immediately detectable due to the nature of quantum entanglement.
This could also provide an answer why we still have hyperspace transport at all, because due to the rather homogenous and simplistic composition of your average ship/module etc., the respective quantum state is in large parts redundant and thus 'compressible', whereas the quantum state of any animated matter such as a human beings(human brains) is unique and uncompressible.
Such a unique quantum state could only be transmitted as a 1:1 copy and the required information signal would be orders of magnitude larger and more complex than that of your average Anaconda, even tough far less particles are involved.
The quantum transfer technology used in 3302 simply isn't up to that task yet.