You may have missed the part with the conversation between James and MC where James clearly states that MC has never been with a woman. He is more focused on his grades and such. During the blowjob, he himself says that he has never done anything remotely like that before. So his motivation is clear, that he simply doesn't appeal to women. Is this clearly stated? No, but I think it's definitely implied enough. Also, for example, with the first meeting with Kimberly where she goes straight to Brian. That's supposed to show that he's simply being overlooked. As for his transformation, I've already included a few hints that it has something to do with a tesseract, but more on that will probably come in chapter 4.
No offence ... this is your story.
"So his motivation is clear, that he simply doesn't appeal to women."
This is more like a "fact", not a motivation.
Is mc attracted by women at all?
Is he straight, gay, bi or is he asexual?
What is the mc's goal?
- To attract (straight) women?
Then changing into a girl doesn't help him since those women are not into girls.
- To change PoV and see the world from the girl's side to understand why mc is not attractive?
That would be reasonable, but only as a temporary change ...
Edit : After playing some more scenes, I have the impression mc's original motivation goes more towards socialising and being friends with the girls and is less about having sex at all.
If women are not attracted to the male mc, there are usually options to try to change this, eg work out, go out, join social activities like university clubs, learn acting, dancing, parties, earn a lot of money and spend it, ...
Such activities usually cost a lot of time and effort ...
MC could start with his servile secretary and go on practice dates with her ... I think that would help, too.
"As for his transformation, I've already included a few hints that it has something to do with a tesseract, but more on that will probably come in chapter 4."
So the title "if i could change" actually means : if mc could be more attractive for women? ... and it just happens by coincidence that a tesseract changes mc into a girl and changes reality so as mc has always been a girl?
Wouldn't it be easier to have mc start as a girl and the prologue is just a weird dream where the girl dreams she is a shy boy overlooked by other people? Then she wakes up as girl and the VN continues ...