Raene was indeed unhappy with her old self, but is slowly growing into the person she wants to be (
with the help of those injections from Ziv and the MC's acceptance). As I understand it, lots of trans people don't go all the way and often don't go for bottom surgery for various reasons. As you say, it could be easily explained away by a pill or some other "future science magic", but it would increase the branching (and associated development work) considerably. Paired with the fact that Raene's current body is a large part of her appeal to most players, I'm going to stay away from more optional branching headaches.