Of course it is. It's completely inconsistent.
According to the EHRC guidance, it is always unlawful and discriminatory to exclude some but not all individuals from services that cater to persons of the opposite birth sex, on the basis of gender differences/ perceived sex/ transition.
However, it is conversely not always unlawful and discriminatory to exclude some but not all individuals from services that cater to persons of the same birth sex, on the very same basis of gender differences/ perceived sex/ transition.
In the first provision it is declared that gender differences/ perceived sex/ transition can never, in any circumstances, be seen as a legitimate basis/ relevant factor in discriminating between people when in comes to the provision of single sex services (i.e. if you allow trans women into female toilets, you have to allow all birth sex males, otherwise it is inevitably discrimination - no exceptions, no contextual factors, nada).
In the second provision it is declared that - oh actually no, gender differences/ perceived sex/ transition can sometimes, in some circumstances be a legitimate basis/ relevant factor in discriminating between people of the same birth sex when in comes to the provision of single sex services (even if the service is for females, you don't have to allow all birth sex female, you can still exclude trans men).
So which is it?
These logics are not consistent, but they very effectively enable the exclusion of trans people from toilets. This is not a legitimate aim.
The second provision aligns with the judgement, the first provision does not.