Maybe the jockeys cockpit where it is sat looking through some sort of telescope or navigation equipment in alien is actually linked to the "head " of the ship, it could be completely biomechanical all in one so to say, thats assuming the giant head is to do with the jockey and not the human side of the plot, it would seem more technologically feasible then, i still think the jockey we see in prometheus will be a different one from what we see in alien, that way scott dosent destroy the ambiguity and mystery too much surrounding it, and it remains shrouded still in partial mystery.