I don't understand how it's transphobia. When you're trans you're just changing from one gender to the other M->F or F->M, right? How does this conflict with thta notion?
A person should feel good about how [they] was born
Ideally, sure, but that's not always possible and telling people that they're not allowed to be trans doesn't stop them from being trans, it only alienates them.
Those procedures ARE psychologically beneficial care and are mostly NOT dangerous, unlike whatever torturous conversion therapy equivalent you seem to have in mind.
Yeah, spreading medical misinformation rooted in bigotry and ignorance tends to have negative consequences when amongst people who know better. Funny how that works.
According to the science, transition dramatically improves mental state and reduces suicidal ideation in people with severe gender dysphoria and is the only effective treatment we have.
So, no, it's not making the problem worse.
As to things "from nature," I'm not sure why it should matter to anyone what chromosomes someone else has unless you're planning on sleeping together. I see zero downside to allowing anyone who wants to, to live as a man or a woman. Nothing is lost, and the person involved gains mental health.
Besides, allowing people to describe themselves how they feel best fits their person is a core element of basic liberty.