So touching on the Madame X being Melia, Maria, or anything along those lines. In the archive under..route 6? The one where it speaks about the interceptor's core. In the bottom right corner theres a book speaking about the Archetype's Influence which notes those who are "possessed" gain golden eyes, skin and hair. Which makes sense with Melia being blond along with her siblings. It also mentions that those who have the power removed have their original appearance restored. So maybe Madame X did have that power in one way and another then lost it which caused her hair to be..black? Its been awhile since I finished the pyramid fight.