There are some ideas so absurd that only an intellectual could believe them. (Orwell, of course)
I'm not a big fan of citing 'common sense', partly because it does actually track IQ, but I think this might be an occasion for it.
99.8% of birth registrations correctly align with gonadal sex.
Of the 0.02%, some will develop an adult female external phenotype which matches their paperwork, and no issue will arise.
Some will develop an adult male external phenotype which doesnt match their paperwork. Whether they choose to correct their paperwork or not, they are protected under the perceptive discrimination provisions of the Act. By the same token, they can be excluded from women-only spaces as an exception to the bar on perceptive discrimination (exemplified in the judgment by reference to transmen, but the same reasoning applies).