I wonder if the seemingly conflicting pieces Mari's origins throughout the films are intentional. Mari is like one of those people that likes to give off an air of mystery and make themselves seem cool, so they are always bullshitting and coming up with all kinds of crazy lies about things they have done in the past. All those weird and pretentious sounding names like Illustrious Makinami and Maria of Iscariote, it's all a facade Mari puts on, along with her quirky personality. She wants to keep you guessing about her past, because in reality there's nothing interesting about it. For all we know, Mari's origins might have been nothing special. She was someone that got tired of their boring and ordinary life, and decided to change it.
Mari is stuck in a delusion, one she creates around herself to escape from reality. It's just like a certain character in another film Anno created, which I believe he might have taken some inspiration for in regards to Mari. The film in question is Shiki-Jitsu.
https://en.wikipedia.org/wiki/Shiki-JitsuIt's a live action film focused on two characters, a director and a quirky woman he meets. In Shiki-Jitsu, the woman has a very quirky personality like Mari, and is living in a delusion. She has lost touch with reality and is always escaping to a fantasy world, one of her quirks being to say that tomorrow is her birthday, every day. She's stuck, unable and unwilling to move forward. Perhaps Mari is the same as the woman in Shiki-Jitsu. She's living out her own personal fantasy. Giving herself all these crazy names and act quirky, piloting the Evas, it's all a game to her. Mari is a woman that doesn't want to grow up, because doing so would mean leaving behind her delusion and returning to her boring life.
Like the woman in Shiki-Jitsu, she has chosen to keep herself trapped in this one period of her life. Chronologically Mari may be 40, but her soul is still that of a teenager, refusing to grow past that stage in her life, her frozen physical age being part of it. Maybe that's why Mari went with Shinji, because like him she too needed to do some growing up. She and Shinji might not be so different after all. They're both people frozen in time, but together they can help each other grow. Why is it that Mari didn't turn into an adult the same time Asuka did, but instead when Shinji did? Because they're in the same boat. It all makes sense now. Shiki-Jitsu also features train tracks prominently throughout it, and it is at a train station where Shinji and Mari meet before the final shot of the movie. The final transition shot is to live-action, and Shiki-Jitsu could be seen as the story of what happens next, Shinji and Mari turning into the man and woman from it who must return to reality together.