I disagree. Here's why.
1.) The burglaries do not have as much in common as people have come to believe. Of the six burglaries alleged against Guede, only two involve possible climbs, along with the breaking of windows: the one at the Brocchi/Palazzoli law firm, and the one at Via Della Pergola.
Two others (Christian Tramontano and Guede's neighbor, Maria Diaz) involved Guede gaining access through an open or unlocked lower window. It is not known how Guede gained access for the two burglaries at the Del Prato Nursery in Milan, but there was no broken glass and presumably no climbing (he was living it up on the first floor).
2.) There are some notable differences between the burglary at the Brocchi Law Offices and the one at the cottage. Access to the window (which was actually a door) at Brocchi's was much easier than access to Filomena's room. The door was located on a balcony, and metal grates below the balcony appear to make it a very easy climb:
http://www.amandaknoxcase.com/wp-content/uploads/2014/02/law_office_window.jpg
In the law office burglary, the burglar, presumably Rudy, carried the rock with him to the balcony, used it to break a window, and then left it on the balcony. Obviously at Via Della Pergola, the rock went flying through the glass into the room.
At the law offices, the burglar laid two men's business jackets on the floor to avoid stepping on broken glass. At Via Della Pergola, there is not much on the floor to prevent someone from stepping on glass, yet there is no crushed glass as if someone had walked on it. There are no footprints, little debris, and there is a plaid cloth bag standing directly in the path from the window to the bedroom door, which surely would have been kicked out of the way by someone stumbling through there in the dark. (Photos on Injustice In Perugia -- scroll about two-thirds of the way down this page:
http://www.injusticeinperugia.org/RonHendry------2.html.)
3.) There has never been any definitive evidence of forced entry through the window. It would be impossible to climb a wall like the one outside Filomena's room and not get your feet and hands dirty and dusty. Yet there are no tracks or fingermarks; what little loose material or dust appears on the floor of the room could easily have come from the rock after it hit the floor and rolled into the bag, or from the broken pieces of window and window trim.
4.) There are two examples of people trying to show that it would be easy to climb into Filomena's window, but neither of them shows anyone actually doing it. One is a photo, and one is a video. The photo shows a guy with his feet on the window below and his hands on the ledge of Filomena's window, but it does not show him pulling himself up.
The video is edited at exactly the moment the climber (different guy from the photo) would have pulled himself up. It cuts from him starting to pull himself up, to the next scene, where he is sitting on the window sill. It does not show how much difficulty it may or may not have taken him to get to the windowsill. Why not?
5.) Filomena is a liar and a low-life who turned against Amanda. She said her room was tidy, but obviously, it was not. It does not look like a room that has been rummaged through -- it looks like the room of a young woman who leaves stuff on the floor.
6.) Rudy going in through the window does not survive the test of Occam's Razor. I think most people here would agree Rudy was a relatively unmotivated fellow -- that's why he started burglarizing in the first place, allegedly. He is an opportunist, not a go-getter.
Why go in a window when you can kick in a door with a faulty lock? Why go in a window without a balcony, when there is a window with a balcony just around the other side of the house, where no one can see you from the street? Why go in an upper window of a place you haven't been to, when you can go into a lower window of a place you're familiar with, and that you know has pot plants?
Why break in at all, when you are just out wandering around, and one of the occupants of the cottage happens to walk up at the same time and, distracted by trying to call her Mum, says, um, yeah, I guess you can use the bathroom?
7.) There is no basis whatsoever, other than Rudy's own account, for believing that he was sitting on the toilet when something happened -- in his version, Amanda and Raffaele came in, and in "our" version, Meredith came in. Again, with Occam's Razor -- if you just climbed in a window to commit a burglary and you're interrupted, why not just be quiet for awhile, and then jump back out the window? Maybe because you didn't come in through the window in the first place.