While the final episode is inconsistent with what was revealed in all other episodes, it's also inconsistent within itself.
One moment, Caine is pulling the blue AI out of his head and giving it a final sendoff: saying he'll miss it, waving goodbye, it disappearing into the void, sad music, etc.
10 minutes later, we see Caine has it trapped inside a cabinet. Why?
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10 minutes later...
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Edit so I don't double post:
I just went back to rewatch that scene and lmao you're right! When Pomni is hugging a hyperventilating internal Jax and telling him to stay with her, his abstracted form stumbles backwards from the emotions of what's going on inside. One foot knocks over a few flash grenades randomly lying in the hallway where their rooms are. His foot knocks the flash grenades against each other, they explode, and internal Jax is now exploding. And that's the end of Jax. He's now a docile dog.
Idk maybe it's not poor writing, maybe the message of random flash grenades lying in a dorm hallway is just so DeEp and mEaNiNgFuL that we shouldn't question it.