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So apart from the presence of a virus in Geneva (which I find likely), you are suggesting that Old Ge's escape was planned by the Source Brain from the beginning. And as a consequence that the robot city apart from the trading center, was a honeypot for people who can potentially discover Source Brain secrets. Interesting possibility. Although I think it's unlikely. Setting up a trap exploiting idealism seems unreliable on the Ashlands. I don't think that even the Source Brain can judge/predict people to this extent based on a short interaction... unless he has awakened.
Yeah, if not for the non-matching timelines (unless this is a prequel set in ancient times - time since Old World destruction and Original Creator split does not match) and power system (which could be explained in far-fetched manner by lack of characteristics and influence of serfirah), I would have said that author is tricking us and this is LotM2. As you said, many things do match. For example location, which is clearly Asia. Western Continent is Asia in LotM (it is to the west of America, where Loen, Intis and other powers are). The author said multiple times in interviews that second book will be placed there. SJ powers also partially coincide with author saying that the main character from the second book will be of the hunter pathway (Inference Clowning from Conspirer, Corny Person for Provoker).
Mostly a guess: I think it was supposed to be a stye and it's the usual infantile SJ behavior. He might reference getting a stye from inflammation caused by an eye strain (hence he closed his eyes to relieve them). Or there might be some sort of belief that one gets a styes from watching perverted things.