OK. So much to say, but here are the boiled down salient points from my perspective:
The columnist has conflated three separate protected characteristics from the Equality Act: (biological) sex, sexual orientation and gender reassignment.
All students, including transgender students, are protected by law against discrimination under all three. Unlike sex or sexual orientation, gender reassignment may result in children and young adults following a medical pathway to change their body to "align" it with a perceived "gender identity".
An early step in gender reassignment is "social transition", which can include a new name or pronouns that are chosen by the child to match their "gender identity". The NHS-commissioned Cass Review has stated in its interim report that social transition is not a neutral act and can lead children to "lock in" on an identity. To align with an identity, a number of children will pursue a medical pathway which "pauses" their puberty using puberty blockers. The NHS has advised that puberty blockers result in loss of bone density and has an unknown impact on a child's developing brain. If the child continues on the pathway to take cross sex hormones (available at aged 16 in the UK), they will be sterile and can expect a significant loss of sexual function. There are other physical changes associated with puberty blocker and hormone use which are also irreversible.
According to the UK gender clinic (GIDS), 98% of children who take puberty blockers will continue on to cross sex hormones. It is imperative that schools involve parents in safeguarding practices, where any child requests a social transition, so that parents may support their children to make the right decision about their future.