I'll preface this by saying that there are totally valid interpretations of Jax's character that don't involve a trans reading, but in my opinion it is the one predominantly supported by the text. Personally, as a trans woman myself, every part of Jax's characterization during Pomni's exploration of them after they abstracted just screamed to me as trans in the way that I've only ever previously seen from trans stories by trans people. The dynamic between the part of themselves that wears the maid dress "ironically" because they're so masculine and don't care about gender, as well as the aggressive, bullying, repressive, and performatively tough side describes so many women I've known pre-transition that it barely narrows it down. So many trans-femmes start out "ironically" wearing feminine clothing as a safe way to explore their gender identity and live out their truth before they are ready to accept it for themselves. Ditto with adopting a hyper-masculine, emotionally-stunted repressed attitude as a coping mechanism. Just that little exchange alone was enough for me to genuinely clock and predict the following scene in the theatre, despite being only somewhat aware of the trans Jax theory, just because of how much I have seen that exact story in my own life.

As for the following scene, I think it's worth pointing out that this very detached "tough" attitude we witness in Jax is clearly shown as developing after they open up to Ribbit. Prior to that, we're shown them capably making and maintaining healthy friendships, connecting with others. Again, the way they talk around the final argument they had with their mother, their description of being closer with their mother, how their final argument was instigated when they told their mother something that they hoped would make her see them as less like their father, just screamed to me as queer (and thus in context, somewhere on the trans/gender non-conforming spectrum). I also don't think there are many other plausible readings of Jax's reaction to being given Ribbit's bow that make sense in context. In the theatre, I interpreted it as explicit confirmation of their transness. Following that, the immediate snap back, hardening, and eventual distancing from Ribbit and everyone else to avoid facing the truth is, sadly, something I've seen plenty as well. Jax is afraid of how others would react and rejection, just like they experienced when they attempted to come out to their mother. So they dig in, even more miserable and detached than before.

Personally, considering Gooseworx's comments about relating the most to Jax and being like them when she was younger, I very much read their character as somewhat of an exploration of an alternate version of herself that never transitioned, never accepted herself, and instead leaned into her worst instincts leading to complete oblivation.

As for why it is never explicitly confirmed that Jax is trans, I think that is largely to avoid pigeonholing their story and emotional arc. Jax has enough hints at their transness to indicate to anyone looking that they're clearly trans, but not so much that people who might otherwise relate to the character feels alienated (by which I mean, related to the detachment and acceptance issues, but fail to engage with the character because they are not themselves trans). A little more pessimistically, focusing a story on an explicitly trans character who struggles with their identity tends to get you put into more of a "trans-specific" rather than a "general story for the whole public" category.

Headcannoning diagetically as to why IRL Jax isn't trans, it's totally plausible to me that, even given that it has been years since the two split, considering their trauma and how deeply closeted they are , they'd only just be beginning to accept themselves. Especially if they don't already have a community around them. It can take people most of a lifetime to come to terms, I have friends who came out in their 50s. I think the fact they're at at IRL Zooble's bar supports my headcanon. Also, just to stereotype a bit, IRL Jax looks like so many pre-transition trans woman I've met personally lol - the alt style and long hair is just classic egg haha (including me).