You are trying to have it both ways.
Usually it's all "trans identified women are no different to men" and "nobody can change their sex".
Now you are all about using the language of "body modifications" to "sex markers" - to say that it is really "about sex".
What about trans women who have had "body modifications" to change their "sex markers" . Why isn't it really "about sex" for them?
I'll insert your language - it makes no difference to the logic.
The guidance declares that it is discriminatory, and therefore unlawful, to exclude some but not all individuals from services that cater to the opposite birth sex on the basis of body modifications/ sex markers.
However, it is conversely permissible (and not discriminatory) to exclude some (and not all) individuals from services that cater to individuals of a shared birth sex, on the basis of body modifications/ sex markers.
In other words, according to the draft guidance, transsexual people (who have undergone body modifications to change their sex markers can be treated differently to other persons of the same birth sex, only for the purposes of excluding them from services.