It would be a major retcon. It's firmly established that Ziran created Deviants, Nezzar separately created Eternals, and Oneg separately created superhuman humans and Mutants.
And Eternals are tasked with protecting Mutants, as they are mankind.
But sure, bloodlines could intermingle. Even Thena and Kro have kids... unless they've been retconned out.
Ok, it does say Oneg created the X-gene, but not how or why, and the Eternals are going after mutantkind because of a secret they discovered, and they already know what they believed was the truth wasn't. It might be possible that mutants were designed for something that could threaten the world, that like the eternals, they may find out a harsh truth about themselves.