Tinkerer said he set it so the ship happens to be there whenever making a delivery, for simplicity, but canonically it's not always there.Doesn't the ship re-appear for the smuggling runs? I'm not sure it was ever at the docks for significant stretches of time so I don't think it would be a good "base" regardless... though if Tinkerer ever did decide to expand the map it would be a cool portal to explore other areas
marvelfreak3000 Put a permanent sleeping spot for the MC on the ship and players will demand to visit the Elven Realm. Which ain't happening in PQ, though it's not ruled out if there's ever a PQ2. Easier to not put one on the ship at all.