The Supreme Court judgment concerns, among other things, how the Equality Act 2010 (passed after the Gender Recognition Act 2004), protects pregnancy, childbirth, maternity leave and breastfeeding. The Act consolidates various pieces of Equality legislation passed before the Gender Recognition Act, in which there can be no doubt that "male" and "female" apply to the gender assigned at birth, so where the 2010 Act reproduces provisions from pre-GRA Acts, the assumption is that Parliament intended them to be read in the same way as their pre-GRA equivalents.
The 2010 Act uses the terms "woman" and "she" throughout these sections, yet there is nothing to suggest that Parliament did not intend these protections to apply to everyone who becomes pregnant, gives birth or breastfeeds at work, including trans men (i.e. people assigned male at birth) who become pregnant, regardless of whether they possess a gender recognition certificate or not. Had Parliament intended to remove these protections from all trans men, or only from trans men who possess a recognition certificate, who become pregnant, it could easily have done so.
This is one of several examples where the natural reading of provisions in the Equality Act requires the assumption that Parliament intended the terms"woman" and "men" to apply to biological sex (gender assigned at birth) if it's to make any sense, so the Supreme Court found that, for the purposes of interpreting the Equality Act "men" and "women" have to be read as applying to the gender assigned at birth unless the Act specifically says otherwise. This, they concluded, is the only way to read the Equality Act 2010 without rendering much of the Act as it concerns gender completely ambiguous, with no one knowing exactly what their rights and obligations are.
In the UK, it's Parliament, not the Supreme Court, who are the ultimate judges of what the law should be. The Supreme Court have found that when the Equality Act 2010 uses terms like "male" and "female" these should be interpreted as applying to gender assigned at birth, without reference to the Gender Recognition Act, unless the Act expressly says they should be interpreted in some other way. If that is not what Parliament intends, then Parliament should revise the Equality Act 2010 to make it explicit how these terms are to be interpreted in various contexts.
Reading through the judgment I'm struck by the fact that, while almost all public discussion concerns trans women (assigned male at birth but living as women), the Supreme Court concentrates on the anomalies that arise for trans men if references to gender in the 2010 Act are read as referring to biological sex. This, I think, is a side of the discussion that is often forgotten.