Yes, it was an unfortunate that the Guidance left itself open to the accusation of 'getting it wrong', but that particular bit did not refer to the central issue of the SC ruling - which, despite all the toilet-related outrage, was not about who should pee where!
The article linked to in the OP, and the one in The National have both taken a minor point and blown it up to suggest that the entire EHRC guidance was wrong, was admitted to be wrong, and had been withdrawn.
If you read the totality of regulations - not just the Equality Act - it is clear that the
'gold standard' is separate sex toilets, with unisex toilets permissible in some circumstances. People planning or managing public buildings are not only bound by the Equality Act - there are building regs, workplace regs, health and safety regs, which are much more relevant to the rules about toilet provision.
The SC ruling was about the definition of sex, not about the provision of toilets in buildings. Nothing in the EHRC Guidance contradicted the ruling.
Causing confusion is the TRA modus operandi!