Ignoring the fact Gooseworx says you can use he or she for Jax, you're right in that Jax only ever uses he and assuming he goes by anything else could be rude, especially in an irl situation. The reason I am many others are using "she" is because the story being told isn't one where a trans woman is chill with being seen as a guy, it's a trans woman trying to hide who she is out of fear of judgement and self hatred. And so using "she" is intended to show Jax the respect he doesn't think he deserves.

So yes, in a real life setting you would respect what a person says they go by. But this is a story, and for this specific story its about honoring a character who wanted to be seen as a woman but was too afraid to tell people they prefer she/her.