@Dee_215
I think "low self-esteem" does apply to Miyakonojou-san. What she perceives as her biggest flaw is that she a) isn't normal, and b) sucks at pretending she is something she's not. She sees other people easily playing a game of masks that she just doesn't know how to take part in. What's the point of friendship without honesty?
You may be thinking of the timid girls you see in other manga from time to time, who desperately hang onto their position in a toxic group of friends as the one everybody else dumps on, who pretend they're not hurt by the way they're treated and laugh along because, in their mind, being alone and isolated is their only other alternative. Miyakonojou-san is slightly better off than those girls not because she has higher self-esteem, but because she *can't* pretend and laugh along. She simply lacks the ability.
Honestly, Miyakonojou-san actually reads as somewhere on the high end of the autism spectrum to me, but that might be taking it too far.