I've no doubt that they happen from time to time and there is even a small chance that it has happened here as well, but I have to go with the odds, and they are vastly against Amanda and Raff. There never was a 'pact', and Rudy had no real history of violent crime either, but we agree what he was capable of I'm sure.
We've already discussed the huge holes in your preferred Mad Libs about the case. You've still got no explanation for how Amanda and Raffaele managed to be murdering Meredith while leaving computer evidence of being home all night, nor any explanation about how events could have unfolded such that neither of Amanda or Raffaele would have left the scene, called for help, called the police or given evidence against Rudy or each other.
Try to work through the actual chain of events that leads up to Amanda and Raffaele standing outside the bedroom saying "Well Amanda, looks like Rudy has stabbed your friend and housemate fatally, and he's ripping her bra off and sexually molesting her right in front of us while she dies. Time for a cover-up! You get the lamp, I'll go stage a break-in while Rudy showers". I just can't see any sane way of making it happen.
They are all important, and when taken all together, insurmountable. Rudy locking the door kind of bugs me a bit more, saying it can be done is not a valid answer. Rudy just committed a murder, he's likely in a dark hallway with a set of keys he's never seen before, locking a door without turning around to face the lock or even swivel a bit towards the door and lock, sorry, but no way he locked that door, someone else did.
That's the big proof of guilt? Someone locks a door in a way you find unexpected and that means two people with no motive and a strong alibi must have been there? Grinder has already explained a perfectly unremarkable way this can be explained: Rudy stabs and molests Meredith, goes to shower, and then comes back to go through her stuff and locks the door on his way out for the second time.
As for the rest of your Gish Gallop ("the break in, Toto, Meredith's locked door, the bathmat, mixed traces of blood, false confessions, cartwheels or splits, lies and strange behaviour") they're all explained easily enough without invoking anything ridiculously implausible.
Toto was a drug dealer with the threat of prison hanging over him, and a history of conveniently coming forward with vital eyewitness testimony when the police were having trouble closing a murder case. He could very easily have been pressured by desperate police to come up with a story to break Amanda and Raffaele's alibi.
The bathmat has Rudy's footprint on it. As we've already demonstrated, among people not primed to see the footprint either way some people see it as Rudy's, some people see it as Raffaele's, but more see it as Raffaele's. There is literally, absolutely nothing here that needs explaining.
There were no mixed traces of blood, ever. Read the Massei report. There were just places where blood from one person fell on or near a spot that had DNA from another person. In addition Amanda had no injuries that would have bled anyway, so this whole talking point is nonsense on stilts.
The false confession bears many hallmarks of an internalised false statement and was produced using discredited interrogation methods known to produce exactly that kind of internalised false statement. Once again there is nothing to explain.
As for "cartwheels or splits" and unspecified "lies and strange behaviour", we can't tell what you are trying to imply unless you are specific and cite your sources. However the bottom line is that people misremember or act weirdly sometimes, and that this is far, far less improbable than someone being in two places at once or committing a once-in-history impromptu group crime like the one in the Massei/Christiani fantasy.
Add it all up and you haven't even got a mild implausibility, let alone a huge ridiculous hole like the ones in your pet theory.
