I cannot help but think that this is an allegory for someone coming out and trans. And the worst fucking direction that coming out can go. I feel so fucking bad for her
If that's the case, going with the disease angle is just stupid: it's an over-complicated explanation for something as simple as hormone replacement therapy.
Chapter 3 explains exactly why the author went with the disease angle: they want the TS character to become a "genetic woman" and not a trans woman as they exist in the real world.
I want to give the author the benefit of the doubt thinking it's a way to protect themselves, because when Chapter 8 comes along, male readers can hopefully project into the savior/abuser without prejudice, since the TS character isn't an "genetic man" and became a "genetic woman".
A simpler explanation is that the author is navigating their own prejudices when they come up with the disease angle though, because the story becomes very creepy very fast, not just tragic.