There is wriggle room under the section on changing rooms. And it does not suggest that pupils who object should choose another activity. In practice, as it says that arrangements should be discussed with the pupil, a wise school will suggest that the pupil might wish to change in the next, but gender appropriate , room/ space, or in the teacher's changing rooms. or not enter the changing rooms till the " bottom half"was sorted, in a single cubicle loo. There
are always ways.
The key here may be what the guidance says, about " some other pupils may" feel uncomfortable", Those words allow the school to school to suggest,and arrange, a solution, as the other pupils have needs too.
The school managers do not want parents and press deluging the school. Nor governors . So it is in everybody's interest to sort something out with sensitivity.
A not dissimilar situation, in practical terms, occurred in a "unit" I ran attached to a West London secondary school . Integration was the aim, and that meant in games lessons. But some of the pupils had ( forgive me if I give no details) very unusual physical features under their clothes. I can' say more, but tbh not all my staff were comfy with what they were dealing with; it could have been traumatic for other pupils. So our job was to fix it so the boy or girl " took part " in the session with their peers. I'd like to think that those few who did not have , lets say, CP ,but something more visually challenging
, were able to be part of their peer group, for games. Even though they did not actually undress in front of them. Quite. These things need resources, extra supervision, careful use of watches and doors...
Cases such as teachers being dismissed over this may not be telling the full story. It is often the case . It nay be that thatteacher would not follow the school's guidelines.