If I may humbly suggest an idea for handling the uneven allocation of active players:

* I think if the ship has paid duty points for a crew feature like "Crew: Boatswain", "Crew: Navigator", "Crew: Priest", etc., that ship should be entitled to have a character (whether PC or NPC) roll for skills that would be appropriate for the Boatswain, Navigator, Priest, etc. They paid the Duty Points, they should get some value from it.

* If a PC was appointed to one of those positions, someone on that crew should be able to ghost them for duties that are appropriate for that job.

* If no PC was appointed, maybe someone on that crew should be allowed to "ghost" an NPC with appropriate skills for that job. The NPC shouldn't be as good as a PC; maybe comparable to the Servant advantage (trait 2, skill 3).

Just an idea. Feel free to ignore it / modify it as you wish.