another thing is that jon is basically in captivity for the first four seasons. he can’t quit the head archivist position so that makes him. a captive. and the archivist job is intended to make him a victim of prolonged and repeated trauma. it’s not immediately apparent because he isn’t being kept in a literal attic but figuratively he was in the attic. the attic just happens to cover his whole life. and elias is responsible for every assault (by proxy), but since his alignment with the eye, i.e. role as the watcher naturally precludes him from getting personally involved in any of it (“My inclinations, predictably, were more toward watching than doing the deed myself.” - mary keay in MAG 62), their relationship is operating on this weird and ambiguous note where jon is aware that elias is responsible for his captivity but he’s never been subjected to the experience of elias personally hurting him. he’s very condescending and paternalistic with jon (father moment) but he just won’t. do that. in s3 jon knows there are monsters out there who want to hurt and kill him, but not elias! elias is the only one he can look to for any semblance of protection, elias is the only one he can ask, “am i still human?” because you see. he has absolutely nowhere else to go.
And I think that’s partially why Jon has never truly blamed Jonah. Like rationally he obviously knows Jonah is to blame, but emotionally he never seems to acknowledge the extent of Jonah’s abuse on him.
Isn’t it interesting that when Jon confronts him at the end he’s not taking revenge for himself, but only for other people? Especially considering that in the same season he repeatedly takes revenge on other people who hurt him?
And Jonah’s lack of direct action against him plays so well into Jon’s guilt complex! It makes it so much easier for him to believe that he’s responsible for everything, which obviously makes him miserable but also ‘helps’ him to deny the fact that Jonah has literally made an object out of him (an archive, not an archivist) in order to use it for his purpose. Until he has guilt he has agency.
So he never confronts Jonah, not really, even when he’s more powerful than him! And I’ll never get over it.