I would say there's no way the first mutilation incident could reflect internalized transphobia, but you could definitely read that into the second incident. Berry is feeling freaked out by the way his body has changed since he's been on female hormones. In the context of the novel, it has to do with a lot of other stuff besides the fact that he's grown breasts, but yeah, he's partly feeling freaked out by his own trans-ness. I think it's important to talk about internalized transphobia, because most transpeople have dealt with it at one time or another. It's pretty impossible not to feel some self-loathing at times, when you have the whole arsenal of our culture aimed at telling you that you're sick or disgusting. Admitting to those feelings isn't the same as validating them, it's the first step to confronting them and telling them to go fuck themselves.

Tennessee Jones: The sister (who as an adult marries into wealth and denies not only her working class background, but also her family) is portrayed negatively because she doesn't necessarily reinvent herself. Rather, she capitulates to social pressures to feel ashamed about the employment and circumstances of her family. She denies her history without making peace with it, and cuts off contact with her family because she is unable to deal with her feelings regarding them. I don't think it's fair to always criticize people who "move beyond" the circumstances they were born to as betrayers, but in the case of this sister, it's apt. She traded in a relationship to her past and family for a new house and a clean slate, without any critical analysis of the value of any of these things.

The thing that separates the character of the sister and Caleb is self-criticism. Caleb is almost painfully aware of his surroundings, his conditions, and his desires. He tries with everything in him to confront the painful things both within himself and contained in his history. One of the big moments of transformation, or reinvention, in the story is when he goes home to his father after transitioning, is beaten up, and finally understands he has crossed a threshold that he cannot go back over. And, from that moment he moves on to shape the rest of his life.

Many of the characters in the book try to change their circumstances and fail, and much of the book is about how people deal with failure without being able to imagine new possibilities for themselves. It's unfortunate, but I believe this is indicative of the reality most people experience. Most of us live our lives pretty quietly, battling our shortcomings and fears, sometimes finding the strength to go after our dreams and desires, but more often lacking even the understanding of what those things are. Often following a strong desire, whether it's for writing or building cabinets, allows people to transcend their circumstances, to move beyond what might have been expected of them.

Also, that really was my experience as a choirboy: all the choirboys were sarcastic and profane as fuck. And then we would turn around and channel this awesome beauty and power that at times really did feel spiritual.