I've name changed for this. I am a lawyer and I also work in the civil service.
Ben C's summary is very clear and accurate, as you'd expect.
The SC was only looking at the interpretation of the Equality Act, not other legislation (such as the Workplace Health and Safety Regulations). Specifically it was concerned with whether the effect of the GRA was to amend the definition of sex in the EA to include certificated sex as well as biological sex. They found that this was not the effect of the GRA on the basis that an expanded definition of sex would render the EA unworkable.
A court would have to go through a similar process with other legislation where definitions of sex/women/men feature, and I think it highly likely that the Workplace Regulations will be next in line. This will need to be a separate analysis to that undertaken by the SC. However a court is likely to follow the same approach as that followed by the SC.
My view is that a court is likely to find that the Workplace Regulations definitions of sex/men/women are biological, as the SC found in respect of the EA. This is because the requirement for single sex toilets/changing facilities in those Regulations is for reasons of safety, which is one of the reasons for analogous single sex exceptions in the Equality Act (such as the exception for communal accommodation and generally for single sex services). It is also the case that the provision of sex-segregated facilities, although mandated by the Workplace Regulations, is only lawful under the EA because of the EA exceptions. Therefore it would be a perverse result if the two pieces of legislation were construed differently.
It's also always worth remembering that these arguments only relate to people with GRCs. There should be no question that people without GRCs should be treated as their biological sex.
Having said all of that, I am afraid to report that the prevailing view in the civil service is that people are desperate to find anything that will undermine the SC judgment. Even in the departments which are subject to Jolyon's JR, officials are broadly sympathetic to Jolyon's arguments and I do not trust them to properly push back against them.
I won't give any more detail in case it's outing. I do think the law is on our side, and eventually the Courts will confirm this. However there is a long road ahead.