As best I can tell, Miu's "mother" and "sister" were both born male. After the mother died, the father decided to raise them while assuming the mother role. The older sibling had GID from a young age and basically lived as a girl from before school started. They started getting hormone injections starting in middle school and committed to reassignment surgery in highschool. Because of their family circumstances, Miu was always confused about gender and what it means to be a boy or girl. Their family was always overbearing about them increasing their "girl power" and they considered it to be a form of harassment. Presumably leading to the events of the start where they throw themselves off the stairs. There is something in there about an ancient god that genders that was enshrined at that place. It wasn't until they started puberty that they finally realized they were probably a girl.
When they go back to the shrine, they find the "real Miu" per se. This entire time the current Miu was unable to find anything to confirm the death of their original body. No newspaper records etc. And this is where it's fuzzy, because it's unclear to me whether the original Miu was fully a girl or not. The "real Miu" has a much larger busy and different skin complexion. They also talk about parallel worlds and slipping between dimensions. When Miu goes back to visit the shrine for the last time in winter, they don't find the "real Miu" there anymore and both Yuuki and Akane have apparently forgotten what happened there. Miu also comments that even her memories of the events are quite hazy at this point. So I think it's implied that this Miu is an amalgam of the MC and the original Miu, with reality bending to the situation. Which would explain why Miu now is a futa.
The whole hospital scene feels like the definition of forced drama, but essentially Miu's older sibling was there for yet another surgery to "boost their femininity" and basically be the best version of the person they wanted to be. But there were complications and they ended up dying. I think the intention is for Miu to stop worrying about preconceptions and to enjoy the girly things they like and the boyish things they like and to simply be the best Miu they can be. If that makes sense.
I wasn't reading using any translation help and I was skimming bc of lack of time atm, but when I have time I'll go back over the parts I'm confused on with a screen reader to revise this summary later if possible.