Well the difference in size between the SJ in Alien and the one in Prometheus is understandable. Been over 30 years since that movie and they probably just made him smaller to work better logistically. In Alien the Space Jockey was just meant to inspire a sense of awe, not necessarily to work from a mechanical standpoint.
This pic is a very good comparison of the two:
You can see how even the design of the chair has changed quite a bit, but they're probably meant to be the same guy in the same chair. I think we can just chalk up those changes to different sensibilities, different material, etc, plus the chair in Alien was much older and the SJ fossilized.
I was talking more about the differences in supposed Space Jockey size just in Prometheus itself.