No, an employment tribunal cannot override the Supreme Court.
The judge in this case stated, correctly, that FWS was about interpretation of the Equality Act and does not automatically apply to other legislation. She then decides that the Workplace Regulations only require an employer to control access to the women's toilets to the extent that is reasonably practicable and takes for granted that it is not "reasonably practicable" to set clear sex-based rules and expect employees to follow them. In essence, she says that sex-based rules are unworkable.
She is correct that she is not directly contradicting the SC judgement, but quite a lot of what she says clearly rejects the SC's reasoning. That is not acceptable.
As well as misinterpreting the SC, this judge appears to have misinterpreted Croft v Royal Mail. What she says about that judgement is, in my view, at odds with the actual decision of the EAT in that case. Croft specifically says, "ordinary good practice requires, as it seems to us, that an employer is to be expected to require those who are, or who are believed by him to be, at law males to use only the men’s facilities and those who are at law or who are believed by him to be females to use only the women’s". I do not see how the judge can read this as allowing an employer to permit men to use the women's facilities.
In my view, this judgement will not survive an appeal. The only question is whether an appeal will need to go all the way to the SC to get it overturned.