Just to sort out a quick thought I had, can i delegate an NPC to pilot a ship I own, then have him follow me, flying my own ship, carrying other NPCs that are not in the party?
Once you load the NPCs on that ship you can move them all at once. However, I'd recommend filing them so that there's enough room for you to board, because you can't kick them out at this time w/o A-Sim help. The ship will then follow the ship you're flying as long as you link them as "NPC Controlled" and you meet the criteria I provided you previously: