In this interview with Sandra Felgueiras, the McCanns state that Madeleine would not have been able to leave the apartment on her own and Kate says that the window and shutter were open.
https://www.youtube.com/watch?v=o_KdIKe_Zds
The transcript "SF So you have no doubts, she was taken from the bed?
KM No doubts. A three-year old would not be able to do that.
GM If you are saying, "Is it theoretically possible that Madeleine left the apartment, then yes. Do we believe it and do we think she was capable of leaving the apartment the way it was found and by which exit did she leave, then absolutely not."
So it is possible Madeleine left on her own, but she is incapable of leaving the apartment in the way it was found.
Doesn't that mean if she left on her own someone else had altered the scene before Kate did her check? That's what I think Gerry is implying.
And that is my theory. That there was someone else who entered the apartment after Matt's check and before Kate did her check.
(Kate seems to have a different POV to Gerry. Kate seems to think she was taken from her bed. How did the intruder leave Kate?) She hasn't really worked it out IMO.