if Judges just strictly look at the words which say "for all purposes" a man with a GRC is a woman.
Ignoring the fact that it's clearly not for all purposes since there are several exceptions detailed in the same Act, the words of the GRA are not set in stone and it is still subject to the same legal principles of interpretation as any other law.
This means that, just like every other law, it can be naturally repealed if a more recent law comes along that makes it partly or wholly redundant. The terms of the more recent law always take precedent.
For example, AFAIK the Gaols Act 1823 that set out sex-segregation for prisoners and female wardens for female prisons was never officially repealed. But Jo Phoenix explains how an industrial tribunal in 1995 that meant prisons had to review their policies on creating a mixed-sex workforce effectively abolished the Gaol Act.
https://www.crimeandjustice.org.uk/resources/creation-mixed-sex-prisons-stealth
I also think it was naturally repealed much earlier when the Prison Act 1952 stated prisoners "may be lawfully confined in any prison", so in a stroke of a pen there went the law for female-only prisons.
In much the same way, the argument is that the clear use of sex defined as a man = a male of any age and woman = a female of any age according to the ordinary usage of the words in the Equality Act naturally makes the peculiar definition in the GRA redundant. The terms of the Equality Act must be looked at first, and then we see how the terms of the earlier law do, or do not, fit in with it.
And the Equality Act must use the ordinary biological meaning of sex and woman, because it simply doesn't work otherwise. The Court of Session recognised that themselves when they said all the references in it to "pregnant women" clearly refer to biological sex. And Lady Dorrian pointed out during the hearing that the single definition for woman applies throughout the entire Act - although this fell by the wayside by the time the judgment was issued, so we now have a biological definition of woman for pregnancy and maternity rights in the Act, but a second "GRC inclusive" definition everywhere else in the Act.
Lord Hope, who was Deputy President of the UK Supreme Court, once said during a case that "The best way of ensuring that a coherent, stable and workable outcome is achieved is to adopt an approach to the meaning of a statute that is constant and predictable. This will be achieved if the legislation is construed according to the ordinary meaning of the words used." And once we do that with the Equality Act, all else falls into place.