I think about how Jonah/Elias lost himself completely to the Eye when he became the Pupil but Jon didn’t bc Jonah hadn’t had the same endless struggle for control over himself that Jon did. And like, over all he relationship to Beholding was completely different from Jon’s since the beginning too.
Everything Jonah did, from attempting the Watchers Crown to starting the Magnus Institute to actually completing a ritual with Jon was to gain personal power and become Immortal. His service to the Eye was for personal gain, and he always seemed to act like he was in control of his powers. And so OBVIOUSLY when he became part of the Eye it took over him completely. He probably didn’t even know how to start fighting it.
Compare that to Jon, who’s whole story is him struggling with the Eye, against the Eye, and because of the Eye. He’s never fully in control and he KNOWS it. Everyone around him knows it too, and they force him to keep himself in some kind of check. Even when the Eye itself gives him a directe statement about how he should listen to it, he shrugs it off and says “You need to do better then that to get me to listen to you.” So when he becomes the Pupil he doesn’t loose himself. He doesn’t even loose awareness. Because for all his faults and mistakes, he never does stop fighting.