Jonah Magnus as a character is portraited very… one-sidedly. Which makes perfect sense, the story is told from the perspective of Jon/Archival assistants and you don’t go around wondering about what motivates your mildly incompetent boss and then you don’t go around wondering why the evil man who kept you hostage/ended the world did what he did. He also intentionally plays into this image of himself, doesn’t allow them to know too much of him.
Which is why in season 5 we could have had brief flashbacks to Jonah’s own Becoming. Make his similarities with Jon more obvious while also highlighting their differences. Because Jon is a kind person, who feels compassion for others, so despite how similar they are he would have made different choices. But we would have gotten to see why Jonah made the choices that he made. And also Jon should have extracted a statement from him, making him feel what he did to others (and that would have been enough actually).