The SC did highlight the fact that the legal system is based on binary sex/gender in its judgement so that point would go before the ECHR
From the judgement
“ As was explained in evidence, there is no legislation in the United Kingdom which recognises a non-gendered category of individuals. On the contrary, legislation across the statute book assumes that all individuals can be categorised as belonging to one of two sexes or genders (terms which have been used interchangeably). Some rights differ according to whether a person is a man or a woman: for example, rights of succession to hereditary titles. There are criminal offences that can only be committed against persons of a particular gender: for example, female genital mutilation. There is a raft of legislation which assumes that only a woman can give birth to, or be the mother of, a child, including legislation relating to maternity rights and benefits, health provision and fertility treatment, and nationality. The legislation governing the registration of births requires the sex of children to be recorded. Legislation relating to marriage and civil partnership (including legislation permitting same sex marriages) assumes that everyone is either a man or a woman. The Gender Recognition Act 2004, enacted following the judgment of the European court in Goodwin v United Kingdom, likewise assumes that all individuals belong to one of two genders, albeit not necessarily the gender recorded at birth. Equality legislation protects people from discrimination if it arises from their being a man or a woman.
A binary approach to gender also forms the basis of the provision of a wide variety of public services. The prison estate, for example, is divided into male and female prisons. Hospitals have wards where patients can only be of a single sex. Local authorities may fund rape crisis centres or domestic abuse refuges which offer their services only to women. Many schools only admit pupils of a particular sex. Much of this is underpinned by, or permitted by, legislation.
Against this background, it is apparent that the questions whether other gendered categories should be recognised beyond male and female, including a non-gendered category, and if so, on what basis such recognition should be given, raise complex issues with wide implications. Counsel for the appellant argued that the courts below had erred in treating the coherent treatment of individuals in the appellant’s position as a significant consideration. On the contrary, the courts were right to conclude that the need for a legally and administratively coherent system for the recognition of gender was an important factor.”
Interestingly - although the SC did acknowledge the (unfortunate) interchangeability between sex and gender they also say that there are only 2 of them. So perhaps there aren’t 100+ genders in law after all wink