There are only 3 charges; the first is kidnap, the second is rape and the third is murder. When they reported 'a second charge of rape' they didn't mean the second of two rape charges, they meant a second of 3 total charges.
The dates are set like this because no one can know whether rape and murder would have happened late on the night of the 3rd, or perhaps just after midnight which would make it the 4th. What they can be certain of is that on the 2nd she was alive and hadn't been kidnapped or raped, and on 10th her body was found so by that time she had.
We do have to be careful what we say, so I'll just give a little bit of my take on the situation without saying too much, but I seem to be thinking quite differently to everyone else posting here. The little bits of information we have about his behaviour while in custody make me think that he, at least in the few days after arrest, didn't have mental capacity to formulate a plan of how to get off lightly or spare any details. I think he may have admitted all charges, and that holding off on entering a plea to murder is totally driven by his defence counsel. He seemed like he couldn't hold it together at all.
All my opinion only.