Could take this allll
the way into fanwank territory and suggest that the black ooze was created by the predators or
that predators are actually an offshoot of the engineers.
Note that I'm not suggesting I believe this, because it's stupid, but these options could easily be worked in.
Predators take DNA from creatures that they think will help them get bigger and badder? Bingo, dino DNA Alien DNA becomes black ooze. Engineers then just happen to come across this black ooze and use it for their science magic.
Or the other, weirder option. Engineer goes rogue and decides it wants to hunt things. Using its knowledge of DNA it upgrades itself and becomes a predator. Others follow and soon there's a whole faction of engineers who have become the predator race. This is how they know to upgrade themselves using a magic DNA altering goo - they've already been doing it for thousands of years!
I hadn't realised just how similar the DNA serum in The Predator was to the black ooze until right now writing this post. And if I've thought of it, maybe Fox has (or whatever will become of Fox). Considering that they just released The Predator, maybe they're foolish enough to make this happen. Predators are Engineers, you heard it here first.