Hmm, I don't suppose that room at the very beginning counts. The one where you need duplicator and the 2 heart restore, and constantly using those so you glitch into the floor, then make your way back to the beginning and fall into a small area underneath.
Considering you'd need to glitch in order to reach that room (even then, it was never intended for people to go in there despite a save room being there), I don't think that counts...
If you manage to do that trick, I think it does add to the map, and possibly to the percentage completed.
Hidden Entrance to Underground GardenTried to find a better quality video, but not much success. I know there was one that explains how to do the glitch, but don't remember where it is anymore.