Even if you are determined to relate the concept of the Space Jockeys with the history of the human race:
1. They should have made it more elegant and symbolic like in "2001: A Space Odyssey". So you don't need the whole "ancient aliens created everything and have our same DNA! trope.
2. They (Space Jockeys) doesn't have to be humans, regardless of their relationship with the planet Earth and its inhabitants.
But I agree that this is fiction at the end of the day, and the franchise is not an academic documentary on astrobiology. It's about monsters eating people with some pretentious paraphernalia here and there. In fact, I don't see many scientists serving as consultants for the Alien movies; as in the case of Interstellar by Christopher Nolan where a real physicist advised the writers, despite the transcendental fantasy present in the final story.