I don't know if there really is a "safe" vessel for Bob. The skull is his home, possession of it supposedly gives the holder of it some authority over the spirit that is known as Bob. However what happens if the skull is destroyed? Can the skull be destroyed? Bob has romped about on missions before riding Mister on Harry's behalf, also gotten into trouble because he was free to roam. Mister isn't a vessel yet presumably Bob was safe as long as he came home before dawn. At the moment Bob is given freedom of the castle because Harry is still trying to understand it's wards, but I don't think it makes it home for Bob, the skull is still his home.