"The protected characteristic of gender reassignment only works one way – not being transgender is not a protected characteristic....Consequently schools can make adjustments to meet the needs of a trans pupil without being accused of discriminating against non-trans pupils".
I think this bit is actually correct. It's similar to how disability is a protected characteristic, but not being disabled isn't.
But the legitimate adjustments would be something like allowing a boy with the pc of gender reassignment to wear the girls' uniform. This wouldn't be discriminating against other boys who are not allowed to do this, because they don't have this protected characteristic.
When there is a conflict with other protected characteristics, the other pcs still have to be considered. There is obviously a conflict in allowing a boy to use girls' toilets, since the protected characteristic of sex still applies, so other arrangements have to be found for him. Gender reassignment being a one way pc doesn't mean that all other pcs can be ignored.