It's interesting that they say that the guidance does not support children 'to be themselves'.
This, I think, is the crux of the issue for many who view the proposed guidance as transphobic.
I think they picture a situation whereby a child's is forced to conform to policies and practices based on gendered norms that will cause them distress.
I would like to see a situation where there are zero gendered expectations or requirements in school and for gender to play no part in any decision making or treatment.
In cases where pronouns cause distress, everyone can be asked to use the pupil's name instead of pronouns. Where single sex activities/sex segregation is needed, supports can be put in place to try and reduce distress and discomfort, as is the case for those with additional and different needs in other areas of development.