I'm not going to assume anything about this person's gender, but I think it's worth mentioning that the Japanese government uses violence to erase transgender existence [1], so it may not be a safe place to be non-cisgender.
Unfortunately, there are quite a few things Japan has tried to erase through history, with varying degrees of success. "Silence" is a pretty good novel that touches on one of those things (beware of descriptions of torture / extreme violence).
[1] https://apnews.com/article/9ef16f52e9b94b9a838b17a63c6c1e8d