As you say the definition of rape is penetration with a penis without consent. It is biologically impossible for a woman to have a penis, so the use of ‘she’ for a rapist is not only a humiliating lie for the victim in court, but is utterly inaccurate legally.
Not any more. Over the last few years dozens of 'women' have been convicted of rape. As you say, the law has not changed but the people applying it, in courts and the prision service, have decided to simply behave as if self ID has become law.