For this thread, we are considering Madeleine leaving only by the main door, apparently consistent with the route followed by the S&R dogs just over 24hrs after she disappeared. She did not leave during Matt's visit or make any audible noises of distress.
Why wouldn't she have rushed towards someone coming through the patio door? Wouldn't she have believed that her absent parents were coming in from the balcony?
There has to be some event between Madeleine being woken and her escaping via the front door. I would not think it likely that Madeleine was aware there was a burglar at the kid's window and then running out the front door since the door and the window are on the same side of the building.
We don't know when Madeleine left the apartment. So I would question how you would know: "She did not leave during Matt's visit or make any audible noises of distress"?
Even though I tend to agree with you that it wasn't likely during Matt's check.