I really think it was the way intent that the Jockey was a giant ancient being,as were the eggs and The Alien.
it will be hard to do that if David is now the creator of the Alien.The original Alien was more about a nighmarish creature and it's mystery.
The sequel did away with the alien nature of it and made it more like a firmiliar ant hive.
For the prequels they had to reinvent the whole franchise to keep it fresh,now deling with creating and religion instead..
So they had to obviously rethink a few things from the past to make this somehow work.
But i think it can work.
The jockey was not a fossil ,more of a mummy .
Fossils are mineralized remnants of organic beings ,mummies are the preserved remnants of them.
I think they chose to go this route,More mummy than fossil.
When David bombed the city,the inhabitants were mummified ,just like the ones in Prometheus.
You would imagine the bio suits would be a defense against the goo,but both the suited up jockeys and the ones in robes were mummified.
The Alien jockey and the ones in The Prometheus installation were both petrified,and had holes in their chests.(dont remember if the Paradise ones had the holes) So it would be safe to say a similar thing happened to them.(contact with the pathogen?)
So its not that hard to imagine that they are the same beings and had similar ends.
And as for the size,well they can genetically modify life ,why not themselves?
And why cant they vary in size naturally as humans can?
All in all,i dont is think its a huge deal about the size ,when everything else somewhat matches up.
