Infected Engineer/Infected Human

Milburn had something burst out of him. One of the characters said something like "There's movement in his esophagus" and then there was a violent "birth" but it happened very fast the thing wasn't really shown clearly. I think the reactions would be different because the thing that attached to Milburn layed eggs in him (suggesting that a hatching process had to take place) whereas Fifield was directly exposed to the goo so rather than being host to an egg or embryo of some sort, he just started to mutate himself.

There is nothing to say the engineers didn't create many different types of biological weapons or biological weapons with different safeguards, defenses and mutation capabilities. Not saying this is the answer - just saying it's plausible.

All different situations. Milburn had a cobra-alien force its way down his throat. Fifield just got acid burns and a face full of black goo. (though why the other cobra alien didn't attack him is unknown, perhaps it knows that if he's drunk the black goo, he's not going to be healthy enough to be a host). As for the Engineers at start and end... also different causes (and probably different from the of black goo. The guy at the start is being sacrificed not mutated, so its probably something that works like our own lysosomes in our cells - break down , rather than the bio-weaponised goo, (which, by the way is billions of years later ) which mutates... and of course the Engineer at the end, was attacked by something which had a rather complicated origin. Holloway was infected by black goo.. his contaminated sperm impregnated Shaw, who have birth to the Facehugger. The only way for a Xeno to be born is for a facehugger to be involved. milburn may have burst out later off screen, after everyone had left the Temple. At that point in the plot the filmmakers were building up the the horror of Holloway's death, so puttting a chestburster in would have made it difficult for that to happen, as somebody would probably be attacked while trying to help Shaw move Holloway (I doubt it would be Shaw, because Xenos don't attack anything that is already hosting a parasite.)

My theory is that the black goo being manufactured on LV-223 is a weapon that is suitable to it's environment. This explains why the Engineers were manufacturing Earth's environment in the pyramids on LV-223. The goo on LV-223 was destined for Earth. The base material of goo doesn't change much between its weaponized form on LV-223 and it's life-creating form that we see at the start of the film, but each adapts to what it interacts with. This is why humans and engineers are not identical - we share the same DNA components, but we adapted to different environments. We've seen the xenomorphs do the same in all the films, and this explains why some form of xenomorph will eventually rise from the weaponized goo life cycle, but these xenomorphs are not identical either - differing in all sorts of ways from pedalism to number of digits and thumbs and so forth. Fifield and Holloway were exposed directly to the goo. Thus they became ill/infected and were outside the xenomorph life cycle. We never saw the end result in Holloway, but we did in Fifield - super strong zombie hell bent on killing humans. Making him/it another effective weapon with some xeno-like qualities (speed, strength, ability to scale vertical surfaces, etc). By comparison, Milbun and the Engineer were impregnated by facehuggers of a type (each facehugger evolved in different environments - one from earth worms and one from Shaw/medpod), and each had creatures violently burst out of them. Shaw was impregnated in a different manner than we've ever seen altogether, and removed the fetus (for lack of a better term) before full gestation occurred then put it through a decontamination spray, altering its evolution as well.

Ah, so maybe it had nothing to do with the Engineer, Shaw and Holloway were more responsible for the birth of the proto-xeno although that wouldn't explain why it was in the pyramid on the wall. If the Engineers made us then I feel like they would know what could happen to their goo/creatures given different situations.

Handor brought up a good point. All of the pods inside the main chambers were different sizes while the pods in the cargo hold appeared to be all the same. It's possible that the main chamber was some kind of lab or preserved storage for all of the different experiments.