The details aren't super specific but this is reading to me as Itsuki (Izumi?) being intersex, not transgender or sci-fi/magic. It does happen irl where a person will be born with visible reproductive anatomy for one sex while internally having different chromosomes/sex characteristics that present later in life (here it's showing up during puberty I think, which does make sense).
Living in the US and being pro LGBTQ it does rub me the wrong way a bit how Itsuki was perfectly happy being a boy, but once he developed female anatomy the story just accepts at face value that he's a girl now. If I knew this kid in real life I'd encourage him to explore his own sense of identity, instead of being forced into female clothes, name, and social role. My expectations for manga on transgender issues are basically zero, though, and this manga is hardly the worst I've seen. On the other hand, I've heard that Japan is not super progressive on LGBTQ issues so maybe this response is normal for Japan?
I'm curious to see how the story treats Itsuki/Izumi going forward.