I have already talked about Elias calling Jon the Archivists exclusively and how it does not make sense here but I want to talk about what it means narratively for Elias to continuously call Jon by his name and not Archivist.
First, there is very strong theme of 'us' vs 'them' in the podcast, humans vs monsters/avatars, which is the underlying cause of the conflict between Jon and the Archival staff (something that deserves its own post). But Jon himself has that separation, most clearly expressed via what name is used to refer to him. The Archival staff calls him Jon, the avatars say Archivist. Thus Elias puts himself firmly in the former by only calling Jon by his name, which has a bigger impact in s3, than say s4, when Jon is still confused about his role and what it means. Jon has certain association with what name people use for him, considering the context of the previous times he had been called Archivist. Something Elias takes advantage of, putting himself in the category of 'us'.
This is supported by the fact that those only instances where Elias calls Jon Archivist are in the end of s3, after s3 when he no longer needs this kind of relationship to influence Jon. And the first/last time he does that is very early on, when Jon knows even less.
You could, of course, argue that he could call Jon Archivist for the sake of reminding him of his role and further dehumanising him. But he already does so successfully, without further needing to alienate Jon. And he does do that, kind of, but not with Jon. He does it to Martin, in mag 139, when he says "our dear Archivist", reminding Martin of who, or what, Jon is.
However. I am a firm believer that Elias does view Jon as a person first and the Archivist being what he does/who he serves. In part, it's because he sees and acknowledges their similarities. Elias always views himself as a person, existing outside of the Eye, and thus has the same view when it comes to Jon, who is most similar to him.
The biggest support of this is mag 160 and mag 200. In the entirety of his letter he doesn't call Jon 'Archivist', in the beginning he says "Hello, John" at a point where there is no reason for him to create that sense of closeness. He has won, if he viewed Jon solely as the Archivist, now there is no point to concealing him. Yet he continuously calls him by his name. Same in mag 200, when Jon drags him out of his place as the pupil. He says "John? I-I-Is that you? Uh, I, I was having the most wonderful dreamâŚ.". And while him using Jon's name later could be seen as his way of appealing to Jon's humanity and pity out of fear for his life, at that exact moment he is disoriented and has no reason to fear for his life just yet. He is sharing his thoughts openly (perhaps for the first time in a long time) and at the moment he calls Jon by his name.
