This film to me is more about family than gender transition. Did Bree's Gender Identity Disorder result from the dysfunction in her family? Did it give her the capacity to individuate? Was she so capable that she could handle both problems? Yes, those two problems and the discovery of a son she didn't know she had, and who was himself a handful.
Early in the film (~0:02) Dr. Breitling, apparently a psychiatrist, conducts a (structured?) psychiatric examination of Bree, apparently to determine whether she will undergo sex reassignment surgery. He accuses her of providing the answers she thinks will qualify her. The psychiatrist refers to a mythical "APA category" of "gender dysphoria" which he says must be a "serious mental disorder."
What strikes me about the portrayal of psychotherapy (starting ~0:06) here is that the psychotherapist, Margaret, appears to be treating nothing, certainly not the Gender Identity Disorder, but rather provides support and very skillfully. Margaret tells Bree she will certify her for sex reassignment surgery, raising the question of whether her role is to assess or treat, but after Bree tells her she plans to avoid dealing with the discovery that she has a son, Margaret revokes the authorization. The numerous apparent boundary violations (~0:16 telephone call from NY; ~0:32 another phone call; ~1:31 visiting her in hospital, kissing her cheek) seem harmless at worst, indicated or even necessary at best. Or maybe they are not violations at all.
Drugs, and not just female hormones for gender transition, come up frequently. Bree's son Toby asks for "percs, Vicodin, and anything with codeine" (0:12). Toby's friend provides him with a powdered drug in small pouches that seems likely to be cocaine (0:17). Toby snorts cocaine (0:30). Toby rubs the powdered drug inside his mouth (1:33). Bree's sister talks about her sobriety and fear of relapse. How much do you think her recovery gave her the capacity to support Bree when she herself must have found it challenging to stay healthy while sticking with such dysfunctional parents?
Suicide comes up in conversation several times: We discover that Toby found his mother after she killed herself with CO from a car in a closed garage (~0:29). A character (Bree's sister?) says she would rather "slit my wrists" (1:10). Bree's mother recounts how she tried to have Bree (then Stanley) committed after she tried to kill herself (1:21). Toby and Bree talk about her suicide attempt with half a bottle of Nembutal (1:24).
Bree and Toby join a group meeting of individuals of ambiguous or altered gender (and one "GG -- genuine girl") (0:42).
What kind of family emotional process do you see here? The film seems to portray Mom as the bad parent, but it seems like Dad could have made a difference.