Supposedly part of the ship, but I was a part of a group from years ago, which tried to write a script revolving around the events of Hadley's Hope and there were calculations done along the same lines SM posted (I forget if it was someone in the group or on the News Group, at the time): The measurements don't add up.
That, combined with the original idea for the script, of it having docked onto a pre-existing silo of a much more ancient civilisation (which would then foreshadow the events which would occur to the Nostromo's crew), always seemed more interesting to explore for me.
Either that or the derelict not being a ship, but just a visible part of a large facility - which 'Prometheus' has now remove all fictional possibility of.
So, I'd like to think the cavern is different, both because of the measurements and because that was the original story's foreshadowing intent, but it really could be either possibility. 'Prometheus' did show that the Engineers like to store containers on the ground in a building, apparently ready for loading into ships in a different manner, after all, so, it could still be so.