This is 'guidance' and we've been here before. Like putting a sign up in the park saying "please don't abuse the kids"
"Headteachers will be told to abide by existing laws including the Equality Act and must keep boys' and girls' toilets, changing rooms and sports separate."
Since they were ignoring the Equality Act before there's no reason to suppose this suggestion is going to make any difference
"Ministers ruled out a blanket ban on social transitioning after concluding it would require time-consuming primary legislation and could in any case be unworkable"
So there is not currently any law protecting children from the whims of any teacher, the government can't spare the time to make one and they suspect the schools would ignore that too.
I feel better already.