About that, i have a theory this time around after v12. There is only 1 other character that uses word Father in the same context as Madame X - Alice. Some "Father" locked 3 siblings in the Unown dimension and ordered, however one day their sister, Eriana i believe, left the Unown dimension. Allen and Alice call Erin Eriana, because they think she is that sister, but it doesnt add up since Erin lived with Souta since her childhood. Its obvious where im going with this, at the moment i think Madame X is Eriana.
Another option is that Crescent is Eriana (some storm chasers got different names, like Sandra became Rhodea), but then its really weird that she cares so much about MC.
There are few questions that theory does not adress tho. First and foremost, Allen, Alice, Melia and Erin already complete Archetype symbol, so where does Madame X falls into that equasion? Also who is this Father in the end? Arceus himself?
This kinda turned into Madame X speculation, but i do not think any of the protectors are on her side. And Hazuki remembers us and clearly wanted to talk, so im fairly sure she is on our side for now.