Perhaps multiple origins would would work so prequels could just be a what if, just one potenial string.
One thing I would say is while I don't like the black goo, I did like what W-Y was doing with it in Romulus.
Instead of the "bio-weapons" angle that is constantly used, the experiments are to improve colony living for humans and that does make sense when you consider the threats humans have to deal with when it comes to colonization. Diseases, bacteria and fungi that the immune system would have not recognize how to deal with due to humans not evolving in those environments.
That being said, if such ideas are used in the series or any other alien media that ignores the prequel, they will need to change the compound from being black goo to something else that comes from the Aliens.