thought on sexing the intersexed

Sexing on the intersexed：An Analysis of sociocultural Responsese to Intersexuality is an article related to the newborn babies who are sexual ambiguous or hermaphroditic. In the middle part of the article, the author argues that when doctors perform sex surgeries for those who are born genital ambiguously, how genitals look like are the key point of determining the choice of gender. That is, the gender of a individual will be decided be his or her physical factors. However, isn't it violating the idea that gender come from the person himself instead of his biological characteristics?

Furthermore, one example author uses in the article catch my attention. It is said that one of the twins born in Canada lost his penis during a routine electrocautery circumcision. Doctors then decided to take another transgender surgery to transmute this boy into a girl. However, it is revealed that she never was satisfied with his identity and receive a male reassignment at his 14. This example sort of is contradicted to the idea of gender can be rebuilt and influenced by environment. Though the transgender girl was never told that she was once a boy, and was raised as a girl completely, it is obvious that her real gender was male. So is that an example of gender coming from birth?