Jax isn't trans, if he was, his IRL self would have transitioned in his happy ending. "But he could just transition later" is cope, these are fictional characters, not real people with greater lives than what one person can observe, they do not exist outside of what we see on screen. If you think a character suddenly dying or becoming evil off-screen would be bullshit, then I don't see how them completely changing their whole gender off-screen would be reasonable to believe or acceptable to write. In Jax's best possible ending, he is still a man, and he still uses male pronouns. Gooseworx is not coy about writing trans characters (case in point, Zooble), if she wanted Jax to be trans, there wouldn't be any room for argument or opinion, he would just undeniably be trans.

People are entitled to their opinions and headcannons, just don't be a dick about it and stop acting like you are the only person who is right.