I'm a retired barrister, so there are others here who may be more up to date on the latest developments, but I don't think the legal position is clear cut.
It seems to me there are at least four possible avenues of challenge.
First, a challenge based on direct sex discrimination. If a college describes itself as a women's college, but admits some males on the basis of gender identity, one immediately has to ask what admissions criterion is actually being applied. Is the institution operating a sex-based admissions policy or not?
Secondly, there is the position of male applicants. If females are admitted, and some males are admitted, but other males are excluded, the question becomes on what legal basis that distinction is being drawn. The answer may well be Schedule 12, but that rather assumes the exemption is available in the first place.
Thirdly, and to my mind most interestingly, there is the college's reliance on Schedule 12 itself. The exemption exists to permit genuinely single-sex institutions. Newnham appears to rely on the provision allowing the exceptional admission of students of the opposite sex.
However, if there is a settled policy under which a defined category of male applicants will be considered for admission year after year, it is at least arguable that this is no longer "exceptional" in any ordinary sense of the word.
If that argument succeeded, the foundation for relying on the exemption may fall away.
Fourthly, I can see the possibility of a judicial review challenge. Universities exercise public functions, and a claimant might argue that the college has misdirected itself in law, misunderstood the meaning of "sex" in the Equality Act, or adopted a policy inconsistent with the statutory scheme.