Technically, we don't, because they're not canon and for all anyone knows, it could just as easily have been a building, rather than ship. the original concept was even for it to have been a ship which had docked onto a much more ancient silo, built by an even older advanced species (perhaps one of the reasons why the dimensions are much larger than the external 'hull' would allow for). Ultimately, though, there's no reason to give an explanation. Just explore some new stories. There is no reason there could not be an identical situation on a different world.