Isn't it just magic? Like they explained it. One day her penis just disappeared
That could be the reason too ¯_༼ • ʖ • ༽_/¯
We'll never know~~
The realistic approach would be that Itsuki is intersex. But if this series had a magical element, well... the fact that the only "magical" thing was a sex change, that is boring.
Literally wished the author would just explicitly make Itsuki intersex. It makes no sense for the series to have a "magical explanation" when the rest of the story is modern setting/non-magical.
While reading this, I only have two answers about how she became a female:
1) She's 46, XX intersex
2) She was born with a big clitoris and when she was a kid, it looked like a small penis.
She had menstruation, that's why she has to have a uterus.