It's the pixels that are on (bright) most of the time that should cause burn-in if it exists. The pixels that are normally off (black) would not cause a "darkening" where they were when you flip the phone. In reality, if you have burn-in, then the normally dark pixels should be brighter that the surrounding pixels that are on more often. It's the icons themselves (whose pixels are often on) that you should see ghosts of if you have burn-in.
If you are seeing a darkening where the black areas of the bar was, then I think you are imagining it. If you told me you could see faint images of the back, home, and app switcher button when you flipped your phone, then I would say you have burn-in.