I think relative positioning should only happen for players that were in a computer or similar block. For players just standing around, absolute position should be saved. To make it easy to stay on board a ship, there should be a way to sit in beds or chairs (probably with an invisible block only seen in build mode that links to the desired chair, since it's unlikely we'll ever get modeled stuff), and those would be occupied until the player comes back and exits (or the chair is removed, leaving the player to spawn as if they were in a computer).