The eye wanted Jon so badly because of Elias’ obsession with him.
Wait so. So.
If we accept this as true, which I think we should because it is based and real and good and true, the Beholding is basically a mindless swarm. It’s all feelings and terrors, it doesn’t think. It’s not gonna favor Jon for no reason, it follows Jonah/Elias’ lead because Elias is the one who’s been feeding it all this time. You can see it like Beholding pulls out of his subconscious whatever Jonah really wants and acts it out.
So. SO. Elias’ adoration for Jon was so intense it rung out more in the Eye than his own sense of self preservation. The Eye wanted Jon to remplace him as the pupil because he was so down bad for his Archivist it took over his fear of death. Jon was literally so important to him the Eye interpreted this as “need Jon at all costs, can even sacrifice me I don’t care”
Congrats idiot you bamboozled yourself.