I'm not sure who "they" are in your sentences, but I personally consider myself a male because I have male equipment. I could have surgery and change that, but I didn't. It has nothing to do with my identity, personality, sexuality, self-view, demeanor, philosophy, or anything else. I was born with a certain anatomy and I'm okay with that. I don't fit gender stereotypes, and that took longer to get comfortable with especially with the bullying in my youth. But I've come to terms with that too.

Other people have their own experiences and situations, so what feels right for me may not feel right for someone else. If they want to alter themselves and change their configuration, they are welcome to do so. I'm just describing my personal experience which may be different than other people's.