Here is my thought:
The Engineer homeworld already has the proto-morph, or as I'll call it the Organic Xeno, living on the surface. The Black Goo alters DNA and therefore on the Engineer homeworld it is forbidden, hence the base on LV-223. When good ol' David and Shaw bring the Juggernaught to the homeworld carrying the Black Goo, it alters the homeworld's atmosphere (the pod spores and such) and also the organic Xeno creating something in between the organic Xeno and the classic Xeno we've all seen.
David then plays on Walter's curiosity and gets him to help in his experiments. All this leads to somehow Shaw's DNA, the Black Goo, and..Walter, being combined to create the classic Xeno.
This would tie in all the elemnets we know, plus Prometheus. The mural in the room with the ampules HAD a classic Xeno on the wall, in almost a worship-like stance. The engineers knew that if they mixed organic material and technology, this creates the beast. Therefore, they kept the Black Goo away from their homeworld, possibly because an accidental Xeno was created there and threatened their existence.
This is confusing I know, but I believe there are 3 types on Xenomorphs here, the Organic Xeno that already exists on the Engineer homeworld, the true Proto-morph which is a mixture of the Black Goo and human DNA, and the Classic Xeno which is the Goo, human DNA, and a mechanical contributor...which mark my words, will be Walter. I can see David creating the classic Xeno from Shaw, Walter, and the Black Goo, and then being killed by it, thus closing the circle on creator, creation, and death just like in Prometheus (Engineers created us, we created androids, and our creation was our downfall.)