Okay, now that the finale's out, let's recap:
Following many hints in previous episodes, including but not limited to:
Jax writing "I don't care" on a nametag instead of an actual name,
Him claiming his ears and tail are the "pinnacle of masculinity," only for Pomni to point out he lacks a tail,
Zooble (the canon nonbinary character) saying that they thought Jax would be "into" wearing a dress,
The series creator later saying he was upset about wearing that dress because he "wasn't ready to ask those questions about himself," along with him in a merch ad admitting in his mind that he looks cute in the dress,
Jax referring to himself as "an egg that needs to be cracked open,"
Him snarkily implying that he is jealous of Zooble's ability to change their own body and finds it stupid that they hate it,
His room being colored in extremely pink and girly colors, except for the blue carpet surrounding a pink rug, the exact colors of the trans flag,
We then enter Episode 9. In a flashback, Jax tells Ribbit that his mother projected gender roles onto him and then punished him for it– if he was emotional, he wasn't enough of a man, and if he lashed out, he was just as bad as his dad. He then admitted something "deep and personal" to her that he thought would make her stop enforcing these gender roles onto him. What he said then made his mother laugh at him, and then berate him with deeply personal insults, and then hug him. When he doesn't say what the personal secret was, Ribbit (who is word-of-God confirmed she/they) then puts a hairbow on him– a character who relies heavily on cartoon stereotypes as a coping mechanism, when cartoons making female characters by sticking "a little red bow on the pre-existing design" is a stereotype everyone knows about– and says his secret is "safe with her."
When approached by a male friend, Jax throws the hairbow to the ground, begins to panic, and threatens Ribbit to "never tell anyone," then cuts her out of his life out of fear and repression. In his mindscape he refers to wearing the maid dress as "getting freaky with gender." Pomni finds his consciousness under a pink-lit lamppost and they play a montage of his previous scenes to the song "Isn't She Lovely?", which is about the birth of a daughter. Static appears multiple times in Jax's mindscape, a potential reference to I Saw the TV Glow, a movie about a heavily-implied trans woman repressing herself.
Putting ALL OF THAT TOGETHER. This is a two-piece puzzle. Jax is transfem and terrified to admit it. Just because s/he was not brave enough to say it aloud and Pomni/Caine did not out them to the other characters– and Jax's human form is not obviously Out in a Red State in 2017, Trump's first term– does not mean it's not canon. Leeroy is 22 and still figuring themself out, and is shown with longer hair, alt clothes, and going to Zooble's (canonically confirmed, if you read the article) queer bar. The creator of this show is a trans woman. This is not something that's hard to figure out.
"Does this mean Glitch is telling trans women to kill themselves–" NOOO!! Jax repressed himself to the point of abstraction, then Pomni finds a way to reach him even through his broken mental state, and the gang puts him in a safe and comfortable blanket fort where s/he can relax and get his senses back in order without hurting himself or others. The other abstractions get to be seen being happy and at peace. No, it's not IDEAL, but it's basically like having a mental break that just needs some care and attention instead of Cellar. We do not see any Abstractions get fixed but the episode does leave it open-ended as to how much they will one day be able to be reached, and the characters have eternity to figure it out. Jax finally opens up to Pomni in that headspace and it's far from impossible she can still talk to him in this state.
The way I see it, there's now two readings going forwards:
First reading is the optimistic one: Pomni was getting through to Jax, she only got kicked out because of the flashbang. Now that they're not just sticking the abstractions in a cellar, and they have Jax in a comfortable and enclosed space to calm down and figure things out, it's not impossible she will pull through once she realizes she is deserving of love. And also when she drinks enough respecting women juice to realize that she is a woman and thus she has to respect herself.
Second reading is the one of abstractions being irreversible. And it's that Jax is a tragedy, but her human self does not have to be. Jax repressed herself to death/insanity because she could not reconcile her own gender with her perception of the world NOR could she accept that even as a terrible person she was still deserving of a future, of the ability to grow and change, and the ability to be loved. She died regretting that she'd driven all her friends away and made the world worse for so many people. But Leeroy is still out there. In the real world, Leeroy accepted help and is figuring herself out. She has a job and a friend group and is visiting a queer bar! In one world, Jax was trapped and fell into a horrible coping mechanism that hurt others and herself, and it killed her. In the real world, Leeroy was offered help and took it, and it's what saved her. And even with the idea of losing Jax, there is still a future for Leeroy, and that's where the hope comes in.
It's also not like Jax is the only trans/queer character. Zooble is nonbinary and makes it through the entire show, is given emotional depth and weight to their own dysphoria and character struggles, and then gets to end the show with their human self opening a successful queer bar and their digital self having epic gay sex!! (entire theater cheered and clapped at that btw)