Depending on their perception of Jon, people either call him by his name or the Archivist. It creates a distinct us vs them situation, with the avatars primarily calling Jon the Archivist with the humans using his name. Michael and Helen show that best. Michael the enemy and Helen the untrustworthy ally. Michael calls him Archivist because that’s the most important aspect of him, he is Gertrude’s successor first and foremost. Helen, however, knew Jon, the person, who was kind to her. They view Jon differently, thus they refer to him differently.
Which is all to say, Jonah acknowledges and sees Jon’s humanity, using his name almost exclusively with some notable exceptions (mag 120 when narrating his dream, mag 138 during the conversation with Martin, mag 161 birthday tape) and only one of those is when directly talking to Jon. Now, it’s easy to dismiss it as Jonah falsely presenting himself as an ally. However. There is no need for that in mag 160, instead Jonah keeps calling Jon by his name the entire time. Same in mag 200, not once does he call him the Archivist. Jonah prioritises his own personhood and autonomy (mag 92: “It’s very important to me you understand that no action I have taken has been controlled. I have done everything because I wished to.”). It’s only natural he would have the same beliefs concerning Jon, who he considers similar to himself.