As for the fuel being able to mutate a human into an alien...
Remember that their technology runs on their DNA. A human cannot use one of their guns. Im darn sure a regular human would be unable to fly the ship either if he put his hand in that goop.
So since its all so DNA-based im sure the fule that powers their ships is also chock-full of alien DNA.
This stuff took 20 years to harvest and collect from other peices of technology. Its also powerful enough to power and control the entire giant ship.
So its very powerful and very concentrated. So Im guessing thats why it has such a strong mutagenic reaction if its in contact with any DNA that is not its own.
Thats my theroy anyway. :)