I don't know about the abductor coming in through the patio doors. It's a bit risky as the McCann's were checking that way and it only took minutes for them to get to the steps, so the abductor even knowing that someone had just done a check and left the apartment, didn't know if someone might double back for some reason or other. Unless the person was working for the OC and would not be obvious to someone who saw him/her.
I think the front door was in darkness, I remember reading a statement by a person who had stayed in 5a and said that the front door area was dark and that they actually disturbed a man lurking outside there.
If the abductor had a key then he came in through the front door.
The window was opened for either an emergency escape, to pass Madeleine through, to ventilate the room in order to remove a smell from something used to sedate Madeleine or a red herring by the abductor so that there would be no suspicion of a key being used.
To say that Kate McCann opened the window to fake an abduction, seems ridiculous to me as one, if she was devious to do that then she would be devious enough to wipe her fingerprints off, and two, she said in her first statement that the patio doors were open.