Where I sat at the outside tapas restaurant I could see virtually all the patio door. The tapas group sat in the next window, a couple of tables along. I didn't go there to look but I think they would have seen a good portion of the patio window too.
I am too tired to sort the photo out that I use to illustrate it but it seems they had a pretty good view
1) is a precaution against someone entering via the patio doors ... an instant escape route
2) The group might have seen the patio curtains fluttering (20mph gusts that night) and light spilling out as they fluttered.
3) I stand entirely by that one.
I'm not suggesting that anyone would have dared to use that patio door as an entrance. Only that it could have been opened from the inside of the apartment to create the impression that it had been a point of entry, diverting attention away from the front door/ door key scenario - much as the window could have been used for that purpose. (point 2. in your list of reasons for having an open window).
It would also have provided a viable emergency escape route (point 1.) on the south side of the building in case of entry by the McCanns or anyone else via the front door.
An open patio door could also have been used to create the impression that Madeleine had wandered (point 3.), even though it would have been unlikely for her to have managed to open the heavy doors. (Why would she be climbing out of a window though? Manipulating an unfamiliar shutter system; climbing out and navigating an unknown drop to the ground?).
Why would someone open the window when the patio door would serve these purposes much better?