I think it's entirely reasonable to suppose that the initial confrontation consisted of nothing more than raised voices. And it's also (in my view) entirely reasonable to suppose that if Guede gained control of Meredith with a knife at her throat, she wouldn't have screamed at that point either.
My best guess (and one which I think is totally reasonable) is that the initial confrontation occurred at or very shortly after 8.56pm. I think there was a period of verbal confrontation (about 3-5 minutes), perhaps during which Guede attempted to talk his way out of the situation. After that, i think Guede made a physical move on Meredith - perhaps as she indicated that she was going to call the police. I think that if he had produced his knife at that point, Meredith would probably have remained relatively submissive - which would be her logical best option if she thought that Guede either wanted to show her he meant business, or if she thought Guede wanted to forcibly obtain her keys (and maybe also rob her
I think that once Guede got her onto all fours, he started the preparations for his sexual assault, by removing his trousers and starting to remove her clothing - doing so with one hand while the other hand held her round the neck with the knife against the side of her neck. I think that Meredith might have resisted at this point, when she realised that a sexual assault was inevitable. I believe that she either screamed at that point, or that she struggled and Guede made the first stab into her neck, which is what made her scream out (on balance, i tend towards the latter). Either way, I think the scream is what made Guede perform the deeper fatal stab wound.
So I think that it's entirely reasonable to tally an initial confrontation at (or very shorty after) 8.56pm with a loud scream at some time after 9pm, and for that scream to have been virtually concurrent with the fatal stab wounds to the neck.
I would put it like this. Rudy broke in and was going to the toilet when Meredith arrived home and entered her room. She made the call to her mother. Rudy appeared or she heard him and cut the call to investigate. There was a conversion, since they recognized each other. He propositioned her and/or made an excuse. She told him to leave. He made a sexual advance on her, pinned her on the ground, and straddled her, attempting to force her to perform oral sex (hey, it worked for DSK, right?). She might have screamed then. When she resisted, he attempted to put a knife to her throat to make her submit. She wriggled around and got cut. He may have retrieved towels and tried to staunch the blood, and then pinned her down and raped her. Realizing he was in trouble, he stabbed her again.
Thinking about it from his perspective, he had to make up a story that would explain the evidence he thought would be brought against him, i.e. a scream, his bloody foot and handprints. This story could or could have happened with "Ciccione" his accomplice.