I like the idea of Athena's influence somehow being the cause, it would explain why the two characters of the different routes feel so at odds. Though I would contend essentially all of the things you put forward as signs of imperfection: None of those are imperfections, they're just character traits, and ones that don't cause the MC any real direct and personal stress. And I would point at that as far as I can tell there is no middle ground or friendship route at the moment - From my attempts at playing through it there's no recovering Asterion's trust once he's sent out so the point of him sending him out innocently is moot given that he then goes full Athenian Archon.
But yes, I think reflection is the issue as well. He doesn't have the opportunity to ever express doubts and fears, which makes it seem like he simply doesn't have them. My mind immediately jumps to all of the decisions where he does have the opportunity to go down the Ruthless route, where the choices are presented almost completely neutrally - If you choose a good option, it is not presented as if the MC had a choice there, it's presented as if the MC was always going to act that way, and never had second thoughts.
Honestly, the gold-and-leaden arm-rings thing grates me here as well, because at that point it isn't a choice for the MC. It's fine that it isn't a choice, but it's clear what it tells the player about the MC: He's so saintly he's not even going to put forward any real argument against wearing something that can and quite probably might sever his arm at some point. The contract as put forward only requires Asterion to be bludgeoned over the head before he can say "I want to go out into the valley" and then be dragged into the valley and the MC either dies of shock and bloodless or is an amputee. I wouldn't have agreed to this contract, personally, at all. For someone who clearly has the malevolence of otherworldly entities following him around I actually think it's strikingly foolish of Asterion to suggest in those words - It begs to have the gods punish him directly for his hubris by setting up a torture he designed.