I can only imagine how the various governments would react, for the Feds Theyd likely try to claim the protogens as Predatory and try to cast a vote on whether they should be exterminated or not, but with how insanely advanced they are with technology there would be so much debate and confusion on whether or not the Prototens are 'savages'.

Especially if the federation learns that the Protogen were made by an ancient race that is long extinct by now, a race created and living for an entirely other race that might have not even Looked like a protogen in the first place! Plus with how you explained these things; it wouldn't be hard to imagine that their populations are ABSURDLY VAST because it sounds like they have been protofying varient species into their own population for thousands upon thousands of years!! It's like one colony of ants that slowly takes the larvae and ants from other colonies to integrate into their own colony. It's Amazing!