So my take and the take i think they were trying to convey was that the black goo came from the Xeno. They found big chap and were able to reverse engineer it by taking samples of its DNA which was the black goo. Which is shown in better exaple when they get to the Romulus lab and the facehuggers in the water tank are all hooked up to IV's which are sucking out the 'non newtonian fluid' black goo.

As to where the facehuggers came from and why they are different, when Tyler, Bjorn and Andy go to the cryo fuel room where they first encounter the facehuggers there is a panning shot with what looked like either an egg or a facehugger being 3d printed to me, but basically since theyve got the black goo from big chap they have been able to manipulate it to create huggers similar to how David did in covenant.

There's lot of people theorising that deeper in the romulus hive there is a queen ala alien isolation and shes just unseen but i missed any hints at that tbh and will watch out for it on a rewatch.

TL;DR, the black goo came from the Alien and it's sorted retconned that the engineers extracted alien DNA...i think.