Shimeji might be something like this too. Something to do with isolation and connection.
Strikes me as if there’s two kinda conflicting world-views here. At one extreme we have the literal interpretation that everyone is just a human copied or uploaded into a machine. At the other, everyone is a representation of some abstract concept. Ignoring one extreme to focus on the other feels wrong, but the intersection of the two isn’t easy to see. Giving someone a single cause to pursue like order or freedom works for characters like Sis or the Gardener, but this is a story about the human condition, about a loner opening up to other people. I don’t think it’s reasonable to apply just one concept to nuanced characters like Shimeji or egg.
An alternative is that no humans were uploaded at all, and that it’s either a single computer or single brain that’s simulating or dreaming the entire story by itself. In that sense the story would be like an ancestor simulation, and the “special characters” would be beings whose minds were tweaked by the game-master to bring flux to the world. That would make them like prophets or messiahs.
Another thought is of inter-cognitive feedback loops. They’re in a world where a mind can influence the world, so is it not impossible to suggest that minds could influence other minds? An ordinary person’s actions could be viewed at in a certain way by a lot of people, changing that person to match more like what they were thinking, making their actions even more extreme. In that way you’d get a positive feedback loop, turning only those who strongly stand out from the crowd into vessels for mass cognition. There’s a bit of irony here, in that this world that permits extreme individuality would also force collective will onto some.