The EHRC Technical Guidance to schools makes it clear children are protected under the EA re gender reassignment from the moment they express their intention to transition to anyone and that in schoolchildren, this intention is likely to be expressed via a change in clothes etc.
On the face of it, this makes sense. Why should a child be treated differently because of the clothes they wear?
But what is bewildering is the choice of comparator for deciding whether a person is being discriminated against. The comparator is an otherwise similar person without that protected characteristic. For a visually impaired person (PC: disability), a sighted person. How on earth were rational people persuaded to use a female person without the PC of gender reassignment, as the comparator for a male person with the PC of gender reassignment? That brings in yet another PC: sex.
The GDST's stance is the only rational one: using a person of the same sex as the comparator. They won't treat a pupil of one sex presenting with a (potential or actual) PC, less favourably than any other pupil of the same sex who does not present with that PC.