Respectfully, but I have a completely different opinion as to why Jon keeps calling Elias “Jonah” in the last season as I feel like most of the je fandom on tumblr.
So like, for me, Jon is SUPER Eye. He always was, I feel like he was even more suited towards the Eye than Jonah, he’s more after the concept of knowledge itself than after the goal of using the Eye to defeat Death and reign all-powerful.
So, when Jon keeps calling him “Jonah” I don’t think it’s to distance the both of them, to deny the man he knew as Elias is now their enemy and has to be defeated at all costs. I just don’t feel like it works with Jon’s character, it just feels… Wrong, to me, to have him be so firmly in denial and never have it be solved.
I think instead, he’s using that name because it’s the truth. Using someone’s real name, acknowledging their real past and accepting it, is more important to him than anything. He’s seen behind the curtain; he’s seen Elias’ real self, secret identity, revealed a mystery and gorged himself on knowing parts of his story and the reason why he became like that. He’s not going to go back to using a borrowed name, because it’s not the truth, it’s someone else, it’s a pretense and an act. “Elias Bouchard” is someone he thought he knew, yes, his boss who was nice but kind of useless, the normal guy with all the edges softened down. Jonah Magnus is who he actually interacted with, who he admired, the one who is so irritating and mysterious but has a grander purpose, the one who parallels him in so many ways and feeds his obsession for the Eye and his powers, the one who is a monster too and accepts it, the one who tells Jon “It’s fine. What does it even mean to be human?”
It’s, to me, acknowledging Elias’ real identity as a body-hopping monster and loving him anyways.