That's a big reveal about Legion and Proteus, and one with some potentially massive implications. At minimum it makes Age of X and Age of Apocalypse both directly, if unintentionally, the result of Xavier and Moira's machinations. It also changes the optics of their relationships hugely, not only did Xavier have a relationship with a patient he was counseling, he did so not out of misguided love but as part of a eugenics project. Moira's relationship is even more messed up, as at best, her eugenics project trapped her in an abusive marriage (and one out of implied rape).