I don't think she is part of any cults either. I also don't believe she is an MK Ultra victim. Mostly because if she was, she would show more signs. She would have erratic behavior and just overall strangeness. Just look at Britney Spears breakdown she had. Butterflies are prevalent in her career as well.
I would agree with your theory. Regardless, Ayu seems to struggle with facing reality. There are a lot of lyrics about suddenly waking up and seeing the big picture and being hurt by it. Then other lyrics about turning the pain into strength and learning from it. Her videos aren't quite haunting anymore because I think she is more emotionally stable now. More grounded and in control. Which makes me glad to see.
The duality section is examples of two opposites. As in Song 4 U, it is light Ayu versus dark Ayu. In Angel, Ayu was kind of the dark angel, surrounded by white angels. In Sexy Little Things, almost everything is black and white. Black and white can mean many things. Pure versus tainted, good versus evil, darkness versus light.