Interesting. The imprint is there because I ran the back of a pen around it. Did you try sticking a blade or paperclip to it? Maybe like you said, only the black has the magnet.
Tried that no metal clings to it, I am thinking of glue gunning a small magnet to the flap. I am curious though on the magnet where is it supposed to make contact with on the iPad, is it on the small inner part of the iPad frame that's visible? Or does the magnet actually make contact and go through the case?
Hope that makes sense.