My reaction to that is that it's all very well talking about what is "unlikely", but you have to make your conclusions based on what has actually happened. What I see in this discussion is PGP (and even judges) asserting or implying that such-and-such interpretation of the evidence is "unlikely", so as to back up their own favoured interpretation which is even more unlikely.
IAC, I don't necessarily agree with your assessment of what is "unlikely". Amanda reports an irrational hostility towards her, from Monica Napoleoni right from their first meeting on November 2, when she (Amanda) became confused over whether the faeces was still in the toilet.
Not only that, but the course of the investigation here follows a pattern visible in police behaviour whenever it has led to a wrongful prosecution. It's a conscious or unconscious effort to "solve the crime" the easy way, by picking out suspects for arbitrary reasons from the people they are already in contact with - instead of taking a step back and telling themselves that the real culprit has almost certainly made himself scarce.
That's why I don't go along with the claim that statistics show that murders are usually committed by people close to the victim (read: "people convicted of murder are usually someone close to the victim"); these statistics are going to be distorted by the very fact that police typically focus on exactly these people.
Statistics may be skewed to some extent by wrongful convictions, but it's safe to say that most homicides involve a perpetrator who kills a specific individual for a specific reason. Unfortunately, that fact creates an automatic bias on the part of police, so they sometimes don't recognize homicides that don't fit that pattern. That is why John and Patsy Ramsey came under suspicion to the point where many people still think they killed their daughter. It is why Michael Morton was convicted when his wife was killed by a total stranger.
I remember a couple of years ago, there was a case in Georgia where a woman went missing. Her car was found abandoned. She was known to have had marital problems.
People on the crime boards were quick to accuse her husband, and they did so with great certainty. I saw many comments along the lines of, "The husband did it. End of story."
Then the woman turned up alive. She had walked away from her life in a moment of panic, and no foul play was involved.
The people who posted these comments weren't corrupt. They didn't have a grudge against the woman's husband. They were lazy and complacent. They thought their gut instinct was infallible, so they didn't need to investigate the facts or see any evidence.
Same with the cops in Perugia. Amanda Knox is a friendly but introspective person. Her reaction to the stress of Meredith's murder was to keep her feelings to herself or share them only with people she knew and trusted. She did not participate in social catharsis with strangers or the emotional theatrics raging around her.
The cops were too stupid to understand that, and too complacent to try. They misread Amanda's character and formed a gut instinct that was simply wrong. It didn't begin as a corrupt or malicious attempt to frame an innocent person. Undoubtedly they thought they were doing real police work when they put the fear of God into Amanda and got her to sign two false statements.
That, they figured, would suffice until the forensics came back from the lab. So they held a press conference at which they made a triumphant announcement. It became headline news in two continents.
But when the forensic evidence arrived, it wasn't what they expected. And Lumumba turned up an unbreakable alibi.
As Matt Jones pointed out, everything changes after charges are laid. The cops realized they had put themselves out on a limb and risked looking like fools. That was when the corruption and malice began.