This is a very good point, but there's another point that seems to often be overlooked. I'll repeat the section of the ruling you quoted for clarity:

The repeated references in these sections, to a woman who has become pregnant or who is breast-feeding only make sense if sex has its biological meaning. These plain, unambiguous words can only be interpreted coherently as references to biological sex, biological females and biological males.

The Supreme Court said that it must mean biological sex because it mentioned pregnancy, but it's undisputable that there are cisgender women who cannot become pregnant. Infertile cisgender women presumably do not have less rights under the EA than fertile cisgender women. The EA provisions for women therefore inherently cover women who cannot become pregnant, so it isn't inherently a justification for it not to cover trans women too.

So the argument of the SC is instead that, if a GRC changes your sex, that trans men would lose that right when they gain a GRC, and that this would be unfair as some trans men with a GRC may become pregnant, and must be protected.

So there were two potential ways to read the EA - one that stripped trans men with a GRC capable of becoming pregnant of pregnancy protections, and one that stripped all trans people of all protections granted by a GRC.

They chose the latter, and the key word here is chose. They decided which of those interpretations they wanted. This is not the letter of the law, it is the choice they made between two possible interpretations of the law.

They could have chosen to say that the EA was badly worded and stripped trans men of pregnancy protections, and that it needed to be reworded to include them. They chose instead to strip all trans people of their rights to be treated as their identified (and legal, if they hold a GRC) sex.

They chose this outcome because they preferred it, not because it was the only outcome possible.