Personally, I think the theory where Maria is Madame X is the most accurate.
Look at it: Maria tried to do something in the Marble Mansion just after gifting us our third badge, but Vitus is very alive and well in our present, so it would imply it failed. The mansion was also refurbished into Chrysolia Hotel (seen in WLL) and that's why Karen thought the Hidden Library could be there.
So with an uncounscious Maria, Vitus extracted the archetype and put it into another being (Melia). Melia was probably frozen in time until the conditions to use the archetype were met, but someone (Storm Chasers) freed Melia and gave her to Jenner, who was coincidentally (or not) also rescued in the fire that got Tesla's family exiled (no one could find his body because he changed realms).
Having no archetype, the original Maria was vulnerable to brainwashing by Vitus, and would now be a faithful follower of her "father", having her original black hair. She could also have her own plan brewing, having no choice but to chase after Melia to recover what was once hers.
She didn't want Melia to use the Archetype power, as it meant to waste its power on some "meaningless" missions, so she said that she never hoped to see the events of Blacksteple Castle. She could also have some knowledge about her Genesis Syndrome and knows that overusing the archetype could end Melia's life, and she needs her alive
It's also interesting that in the new version of Terajuma, Angie (Vitus) does something to Melia, which makes her talk backwards and like it's someone (Maria?) trapped somewhere (a pocket dimension made to break her mind, maybe the prologue), whom the Interceptor (MC) has betrayed at least once. This betrayal could mean that the creation of Madame X was necessary for the current present to happen (fixing our mistakes), so even tough MC could have changed something, they let Vitus extract the archetype from Maria