Suppose I have Savage Shores Wraith in my fleet, and he has snagged a couple crew. Can the crew that he saves be unloaded from the ship, or are they stuck there with him?
None of the crew taken that way are forced to stay with Wraith, so you can unload them to islands or other ships using the normal rules.
What all of that extra stuff in his ability and the PC does is protect them from point and cargo restrictions and allow them to use their abilities while they’re still on the ship with him. As soon as they leave (or he does) that all goes away and they return to normal.