Ironically, the most fertile source of legal protection from discrimination on the basis of 'gender' is the protected characteristic of sex. Any attempt by a dutyholder under the Equality Act to require a person to manifest the gender presentation of their sex is discrimination on the basis if sex, and unlawful.
Also, despite the arguably-inappropriate terminology , the 'disability' protected characteristic should cover 'gender reassignment' as it was actually conceived of (and publicly represented) when the GRA and the Equality Act were passed.
Receiving a gender reassignment certificate is tied to a diagnosis of gender dysphoria. The challenges of living with this diagnosis are the whole reason for allowing latitude in the recording of sex, just as the challenges of living with a disability generate the rights to (e.g.) permission to park where others can't.
Under the Equality Act, 'disability' is interpreted widely. I only learnt this relatively recently. I had thought you have to be 'registered disabled' in some way to qualify for protection, but of course all that is required is having a physical or mental condition that has a "substantial, long-term, and adverse effect on one's ability to carry out normal day-to-day activities".
I do understand that the terms 'disability' and 'impairment' (which I think may also be used in the act) are offensive to people who qualify for the GR protection. But there are lots of contexts in which they are equally offensive to people with other sorts of differences, e.g. deafness. To the extent that language generates a sense of stigma or negative judgement, that should be campaigned against in the same way as for other conditions, and perhaps different terms can be evolved (so long as this is organic and not top-down).
If, and to the extent that, gender reassignment does not involve a condition that has "substantial, long-term, and adverse effect on one's ability to carry out normal day-to-day activities", what would be the justification for the special provisions that employers, service providers, and public bodies need to make for people with this PC? The only possible answer to this question is that they must do it in order not to discriminate against them on the grounds of their beliefs. And of course, this is already baked in to the protected characteristic of belief.