What OneEpisode said - they referred to the ONS guidance on using the ethnicity categories from the 2011 census, but haven't taken the same approach on sex.
Stonewall doesn't claim to speak for women so that only covers the gender identity side of things and not sex. They need to look at both sides, not just gender identity, as sex is a protected characteristic and they are potentially discriminating against women by not collecting this data (depending on the purpose, etc).
I would point out the legal and cost ramifications that arose for the government when they tried to scrap collecting sex-based data in the 2021 census and got sued by Fair Play for Women.
Also, their explanation:
For D&I monitoring we are usually interested in gender, a socially constructed concept, rather than sex, which relates to biological characteristics. However, sometimes questions are asked around sex because the Equality Act 2010 lists sex as the protected characteristic rather than gender.
Well, that's fucking stupid, isn't it? Their D&I monitoring doesn't cover sex? Their wording implies that the EA2010 is incorrect and is some sort of mere "suggestion" as opposed to being the key piece of equality legislation currently in force. Madness.
They are looking at public involvement which makes it more surprising they don't want to record in line with the EA.
Are they subject to the public sector equality duty? If so, they're exposing themselves to liability by not considering sex as a protected characteristic.