I just want to finish the thought I had upthread ... if we assume that Guede alone was responsible for the murder, that he was in the cottage after entering through the window and that he then found himself locked in the cottage, it makes sense that he had to find the keys to leave the cottage. He, as with anyone responsible for the murder, had good reason to delay the discovery of the body by locking Meredith's door. He also had good reason to take the cell phones in order to prevent her from reporting what had happened (even though she was too far gone to report anything). He also would unlock the front door with the key and have no reason to lock it, as he would assume that the door would remain closed after he left (didn't know that the wind blew it open) and would have good reason to avoid handling the exterior of the door. The unflushed toilet, for Guede, was probably normal, so it wouldn't have occurred to him to flush several times to clean up his mess.
Essentially, the missing keys and unlocked front door do more to support Guede as the culprit than Knox ... in my opinion. That does not, however, explain the other evidence that points to Knox and Sollecito in the crime scene.