Everyone knows I have my fair share of complaints about the prequel movies, but playing devils advocate here;
I really don't think there's really *that* big of an inconsistency between Prometheus and Covenant when it comes to the Pathogen.
First thing first; there's a lot of assumption here that what the Engineer drinks at the beginning of Prometheus is the same substance as what is in the urns on LV-233. We see a black substance. A bottle of turps looks like a bottle of water without labels. So removing that as a potential outlier for a moment, what do we actually see the goo from the vases do? Only one of two things;
It rewrites the physiology of an organic life form and either 1: kills them, or 2; triggers mutation. That was pretty consistent across both movies.
It appears variables affect the outcome. In humans;
When consumed in a minute amount, infection spreads slowly.
When literally bathed/face-planted in it, mutation is more obvious.
Of course, the weapon wasn't designed to be consumed, in covenant, we see the effects it causes on a population in huge quantities when detonated airborne as intended; it appears inhalation causes a volatile response, with bodies literally mutating and turning themselves inside-out (possibly a result of oxidisation?).
In animals, we know it creates hybrid forms, usually with xeno-esque head shapes (I know someone mentioned the hammerpedes don't have this, but it's that a fair analysis? Worms have no distinguishable head at all, whereas a closed hammerpede head is clearly distinctly a head- I'd say it's pretty much doing the same thing as we saw it do the creatures in David's lab).
The trilobite was an anomaly, caused by pathogen mutated semen entering Shaw... you could say an unexpected surprise in David's 'first experiment' that he couldn't have anticipated, but regardless, it created something similar to seen in the mural.
But I think most importantly, the whole point of the movie was the analogy of Prometheus stealing fire from the gods... playing with something we don't understand. It's not *supposed* to make sense, because it's beyond our understanding; even now, as an audience we are making anthropomorphic assumptions (myself included) to what we think it does/doesn't do, or should do, trying to make it fit with our understanding. It's alien in the truest sense of the word.
That being said, I still believe it only does two things, as David states in Covenant, and as we see across two movies. There are so many external variables involved I don't think it's fair to say it's inconsistent. 😅
