I think that Phill Martin, the engineer, is most likely a stand-in for whatever they plan for the finalized jockey to look like. So, of course it won't look exactly like him. He's just helping the effects crew fill in what they need to so we have a great looking engineer.
And, by the way, from my understanding, the "space jockey" and "engineer" are interchangeable terms. Ridley Scott has said on many occasions that the derelict being never had an official name and that "jockey" got thrown into the mix because of how he was situated on the ship as a pilot to speak. With the new movie, however, it seems that the official name is "engineer," which plays into the whole creation and discovery thing. So I think it's a good assumption that both the jockey/engineer are one in the same and that, for one at least, Phill Martin, a human giant, is playing him.
P.S.: In Martin's video promo, he talks about working out as a hobby so he can physically be prepared to do stunt work at his size. So, he should fill out the engineer suit nicely and help sell the illusion that the beings are larger than life.
