Yes indeed!
You can't confer a fundamental human right to do or have something which is impossible. Like unaided flight, or changing sex.
If 9(1) is a deeming provision, it doesn't matter that sex and gender are used interchangeably. Gender may have been just another word for sex at that time. Plus the Goodwin judgement talks about gender identity, if that is what was meant, the lawmakers could have used that in the GRA or the GR bits of the EA.
IANAL, of course.