If it helps, I teach in a pretty liberal school which is fairly LGBTQ+ inclusive, I would say around 10% of the older students I teach are gay/lesbian/bisexual. Last year I taught two FtM trans students, this year I don't teach any. Maybe it's the area I teach in, but I don't feel there are so many trans students compared to perceptions in the media.
In the past we did have an issue with a student who said they wanted to transition in school but they didn't want parents to know. Our pastoral staff made the point that we could not guarantee this could be kept a secret from parents, because there is always a risk of a supply teacher contacting home, or a student telling their parents in the community. They said if they wanted to use a different name/pronouns in school then it would be much better to discuss with parents first with support from school (worth bearing in mind this was a student over 16)-this is what happened, and I think an agreement was made that they could use their preferred gender/name in school.
It hasn't come up, but I don't think we'd allow a younger student to use a different name/pronouns in school without discussions with home. Generally, it's home coming to us saying "Can you now call them X and use (pronoun) instead?".
If there was genuine risk of abuse, we'd follow safeguarding processes, just as if there was a genuine risk of abuse due to being gay.
I do understand why people are concerned about some of the messaging, but equally you have to bear in mind as soon as you tell teens they can't do something or it's forbidden, it becomes the most popular thing to do.
When I was at secondary school, Section 28 was still in force, and our teachers wouldn't discuss anything around the existence of e.g. gay people. School was a horribly homophobic place. I'm bisexual, and I genuinely think my school experience damaged me for life. I'm glad we can at least talk about these things openly in school.