Boku wa Mari no Naka felt like the author was just kind of done with it. I know he had already started a new series, and you can really notice that he's obviously investing less time on Mari in the later chapters. More blank backgrounds, bigger frames, and the plot progress starts really dragging. It just kinda seems like the author wanted to do his big plot twist, and once that was obvious he was ready to be done with it.
I do still read Mari as totally gay though. Like, in the early chapters we learn about her having a ton of anxiety over various aspects of her life, especially the stress of judgment from her peers, and her attempts to keep up her perfect appearance. That she then has a romantic encounter with another girl could be read as the final straw, she already is stressed out at trying to fit in, now she's learning about her sexuality and realizing she has to hide that too? We know she had already been turning down boys who had asked her out, and Isao also finds girly mags in Mari's closet. You could read it as one reason why Mari envied Isao so much, that his sexuality was catered to while she has to keep hers hidden.
