idk 100% but my interpretation is he wanted nanako to understand who he really was by having the trepanation. but as you can see, her head was bleeding so i'm assuming that she died out from blood loss. in the end, he gets called by the cops because of her death. the manga says homunculi are basically distortions, so he was viewing people based on how he viewed himself. his identity was distorted so he couldn't see people properly. i think the main idea is you can only understand people as much as you understand yourself. i'm sorry if this doesn't make sense.
there must of been some placebo effect which caused him to be hypersensitive with people... so i think he can see people's innate fears or their "core" because of the trepanation, it allowed him to see the finer details of people's unconscious self. the consciousness and unconsciousness is at a finite play with how you interact the world via self. i don't want to get too complicated, but with the larger guy, the MC was paying attention to him. as humans, we are prone to see errors and defects as a magnified scale. his understanding of people was based on inferences, social cues, and environmental factors. it's very intuitive and it helped him go back in time, to see how the trauma played out to now. most of us have an event where it shaped who we are, even if we're different now, nonetheless it created you. i think the manga is supposed to be abstract and most of it is left to your interpretation! ^_^
Mmmmmkay