Jockey looked entirely different and was fossilized and
Androids were not Wolverines with Matrix style combat techniques. This is not my assumption.
Yes, it is plainly your assumption- android models were never shown in combat roles or taking minor injury in the past.
It's also made plainly clear, from Alien to Aliens, to Resurrection and Prometheus that each model is different.
I don't believe the ships we saw in any of the prequels were the Space Jockey's ship, so the discrepancy is irrelevant for now.
They were never on-screen stated to be the same thing, that's just an assumption for now.
Before you start quoting BTS material statements, R.S also said that the Alien would regenerate and we have no evidence of that either;
Whatever the intention may be, that's not what's onscreen.