It would take 10 seconds to go through the door grab Madeleine and take her back out. Skinny man had to get through the window but first get to it and raise noisy shutters with kids in the room. The village idiot would not do that when the front door is next to the bedroom door. Wasting time is not an option with regular checks going on! In and out quickly job done. 9pm Matt get back from check. Gerry leaves. 9:10 Jane leaves 9:25 Matt/Russ leaves etc. An abductor was doing what? Opening windows and shutters and making himself at home 
Snipped...
The problem with going out via the front door was that you couldn't check to see whether the carpark was clear to go across by just peeping out of the door as it was so deeply recessed. So you would be going out 'blind' and by the time you did have a view of the whole car park, anyone crossing would also have a view of
you - carrying a child. Also once an intruder was in the bedroom he would no longer have any idea whether anyone was heading back from the restaurant either to 5A or to another apartment.
We don't know what the intruders intentions were or how long he intended to stay or whether he was going to administer drugs.
IMO there are several reasons for opening the shutters/window.
1. As an extra escape route from the apartment which would avoid confrontation with anyone who may have returned and was coming in via the patio doors.
2. As a means of checking to see if the car park was clear before going out via the front door and to be able to better hear any noises coming from the car park.
3. As an attempt to hide the fact that the intruder had a key.
If the intruder was a man acting on his own, then I can see how any of the above would be seen as advantageous by him.