That's because, as I said, at the core of this game's story is the MC, and like all MC's in adult games, they are the central focus of the LIs even when those LIs are already in a relationship. But in terms of the reality of the story that exists in this game, Maya has found herself inexplicably attracted to the MC, most likely due to the emotional state she's in over her relationship with Josy, and it's caused her to feel a connection to the MC that confuses her. She's not sure what this means because she has been convinced for some time that she is completely lesbian, yet there's something she really likes about the MC. This is why, on the M&J path, this has become a full-blown attraction and romantic interest, whilst on the non-M&J path she knows she likes him but isn't sure in exactly what capacity.
Just because she has an attraction to the MC does not negate the predicament with her Dad and her relationship with Josy because she is still in that relationship with Josy on both paths. Josy is still the person she loves the most and so she's not going to give that relationship up for something that might just be a passing fling or just the result of confused feelings because of the strain this situation has put her under. Plus, on the M&J path, if she were to have her way, she'd be in a relationship with both of them and this still does not solve the Dad problem. So the core of her story remains, regardless of what path you choose, which is that she has an attraction to girls. Her having any sort of feelings for the MC doesn't change that or lessen the drama of her story because her interest in girls is at the root of that drama.
Fiction draws from real life and that's why people can sometimes see it reflected in what they view/play/read. Maya not openly expressing interest in girls is, for me, very reflective of someone I knew in real life and hence why I drew the comparison between them as a means of explaining Maya a bit more. Having these real life comparisons is what can enhance a story or a character because it makes them more relatable and that's why I'd say that any such examples can be quite relevant when discussing this game or any other piece of fiction.
Both Maya and Josy have already found out that Quinn is full of shit and Maya has pretty much quit the HOTs already, so neither will be getting involved with that. Josy, however, may still stay with the HOTs, but her Dad is paying her tuition so she has no reason to join Quinn's little operation.
Because she's hurt. Feeling something for the MC doesn't mean she can't still be devastated at Chad breaking up with her, particularly because it not only comes out of the blue and with no explanation, but she seems to have given a lot of herself to that relationship and she doesn't know what went wrong. She feels that she needs to know that, and he doesn't give a reason, that's why she's pissed and angry with him.
In the words of C3PO, "You obviously have a great deal to learn about human behaviour."
P.S. Press the 's' key and you'll get better sceeenshots.