I think it's really hard to relate that article to anything negative about the guidance. It sounds firstly as though transition has been completely negative for this child and that the school was one that badly needed support with these issues, which the guidance would help with.
Pre transition they were a confident girl, in their own words 'masculine', presenting in a way they liked, enjoying multiple sports. Them raising their gender sounds really badly handled by the school and the guidance would help here - the family are supportive and no safeguarding concerns, which should have been the focus, rather than what the child perceived as a punitive process of contacting the family. I agree the child should have been involved, and if the school handled this better, maybe the parents would have approached the school directly.
Transition seems to have coincided with a plunge in the child's confidence, function and access to learning, no doubt due to the bullying, which the school needed to tackle properly, like all bullying. The child's view that they could somehow transition but nobody would notice sounds implausible and i have to ask what else was going on with them. I also agree that robust bullying policies are the key rather than a big focus on transition.