This probably also explains why the giant head statue looks like a Human instead of anything else.
They seem to be moving away from the "growing out of the chair" comment Dallas makes and the ship not being as old as assumed. I would have prefered keeping in line with the old ideas but this direction could be even better. Plus we have to remember the Nostromo crew could only guess what had happened. In addition to Prometheus not even being thought of yet. This is the bad side of prequels, having to fit into established things later in the timeline.
Although it's not 100% certain that both ships are the same one. It seems like the could be setting us up for a twist where there were two and the one of this film is completely destroyed. Might help to explain why the planet looks vastly different from this film and alien. This one lacks the wind storms and perpetual night of the original.
Now that I looked over the Prometheus wiki article I'm wondering if it's even the same planet LV-426.

Is there any word on this? I know they're using the same star system (Zeta II Reticuli). Perhaps this planet is a different of from Alien/Aliens and is the "main base." LV-426 could be where the Space Jockeys crashed a ship many years ago and just never bothered to do anything with the ship. Kinda like "let's leave the thing alone so we don't get attacked in case an egg hatches."