My own preference has always been that they just say she and her brother are mutants in every way that counts. They aren't the first mutants to have insanely complicated and confusing origins. Why bother to retcon their origins for the 932535th time when there's no difference between them and mutants who got their X-gene at birth?
They're already doing something like this with Magneto, just saying that Wanda and Pietro are his children even if they're not biologically related. And they've been mutants a lot longer than they've been his kids.