When I go to board a vehicle docked on my ship, I get this message:
Warning: Boarding a docked vehicle or ship while the YT-1210 you are piloting is travelling will automatically abort your current trip, which may result in loss of time. Are you sure you wish to continue?
However, I have an RX Pilot droid in the cockpit, it has a Starfighter-Freighter skill of 2, and I am the manager/supervisor of the droid and pilot/commander/owner of the ship. I tried it with an FA-4 droid and it worked fine--and it only has a Starfighter-Freighter skill of 1.