I seriously doubt Police are making up the charges.. they would have forensic evidence that he did rape her in all three ways, if that is there charges- an autopsy was performed. And at this stage as its a committal hearing I am not sure all that evidence will be known to all who were in court yet. You would believe the accused in his denials, but not the police? He is also denying killing Jill, and yet he has previously admitted it and was able to take police to where her body was buried..
I don't see why Bayley would be denying 2 of the 3 rape charges if all 3 charges were iron-clad. He is denying the murder charge because he can claim he is a rapist, though not a murderer- the murder happened as he was trying to shut her up from screaming, though in 'shutting her up', he can claim, he applied too much pressure and she passed out and never regained consciousness; so it was some form of negligent homicide, lacking in intent to kill. How are you going to refute that? You simply cannot- it is possible; though i guess the question boils down to what is reasonable; that is, what is probably to have transpired at the time, something we can discern from past behaviour patterns (that go to character), which is where previous history of offending (if any) comes in. If you ask me, it is not clear to me at all that- at the outset- he intended to kill her, though he definitely intended to rape her. I think it began as a rape and somehow morphed into a murder after she communicated to him somehow that she has seen his face 'out there on sydney road' and can now identify him, which is precisely the prosecution's case. So at that point, the intent to kill her was formulated. This is most probably what happened. It is still possible, however, that he tried to keep her quiet, but in doing so accidentally killed her. I am not sure which happened. I think it is kind of irrelevant which it actually was as he should not ever be released, and the rest is mere semantics- important, though ultimately indecipherable.