What you are highlighting is that the prison service is stuck.
Fairplay for Women have some interesting tweets on this today and they have drawn the same conclusion, it strongly suggests the prisoner has a GRC or they would have been chucked back to the male estate so where else in the prison service can they go?
A MTF with a GRC, who has not been safe in a standard women's prison, all they can do is send them to the Trans Unit at Downview. It's all they have.
Sex offences in the prison world are offences you have a conviction for. So no chance of going to a male sex offender unit. And his index offence, murder, is wrong anyway, not appropriate for a sex offender prison.
Unless the woman involved decided this was non-consensual and brought criminal charges, it's not a sex offence.
Self-ID would be a total nightmare for women and the prison service.