The people running IT determine how data is recorded - including recording Gender rather than sex, and requests for ‘preferred pronouns’. Once these things are baked into the data system it is very difficult to get the system to consider sex or eg single sex spaces of for equality monitoring purposes.
These groups are also lobbying senior civil servants and embedding their belief through training which goes against the law. Or the insert information into reports or codes of practice that hugely impact services such as ‘Appendix B’ that removed single sex wards, or the Bench Book that required rape victims to refer their male rapists as ‘she’ (and get recorded as such in the IT system).
As for going against government directives - we see this constantly. Just look how few organisations have implemented the Supreme Court judgement.