Ship transfer risks being a game-changing unbalancing mechanic, unless it's restricted - cost, time or restrictions on where you can transport too. It should be convenient, but less so than flying the ship yourself - a bit like public transport compared to driving the car.
Assuming ships are moved by Lynx Bulk Carriers, that's a big ship travelling through space just to transport my ship for me. No way is the corp. or crew running that ship going to make any profit with just my business.
I suggest that
LBC transfer only be possible to systems with have populations greater than 1 Million (or whatever seems reasonable).
LBCs not transfer to systems which are Anarchy or have wars going on - there's a risk that the LBC might be captured or destroyed.
LBCs make timed runs, posted on the mission board (or transfer board or whatever...) there's a ship leaving at 18:00 and going to system X, duration is 60 minutes. You book your slot and wait. Popular system like Sol would have transports leaving quite often, transfers to Jaques might only run once a week.
Maybe LBCs run routes like a public transport system (or a multi drop courier) they travel between a number of systems and you can book a slot on one.. if the system you want is the next stop it arrives quickly, if the system you want to transfer to is the 12th stop, it takes a bit longer.
In both circumstances, the drop off point might still be 20LY from where you want the ship to be, so a little bit of flying it youself is still required.
It solves the FSD problem and makes the whole thing believeable. Whereas matter to energy instant transfer just reeks of deus ex machina and is as flawed as Khans cross-galaxy transport to Cronos in Star Trak Into Darkness - what's the point of star ships if you can transport anything anywhere?
Edit: LBCs only transfer to space stations, not outposts and not surface ports.