I agree theories involving woke and wandered are not really plausible given the open window and raised shutter.
In what way do you believe the window is key? Again I agree with you. I believe the perp learned of PF's recent attempted burglary directly above 5A and used this knowledge to stage the window/shutter to confuse/deflect.
The window may have been opened to distract attention from the intruder using a key to enter via the front door.
It certainly wrecks the 'woke and wandered' scenario in my opinion despite the police seemingly concentrating on that scenario for quite some time.
I don't think anyone would have had the foresight to envisage how it would be used to detract from attention to the intruder to focus blame on the victims. That was a truly unexpected bonus which to my mind irretrievably damaged the investigation into Madeleine's disappearance. That in combination with the demonisation of the only witness Jane Tanner must have meant the perpetrator could not believe his luck.