I don't know about you but the design of the apple cover was fine until I started using the dock, then all of a sudden it wasn't such a good design after all as it will not fit properly when the ipad is docked.
This afternoon I got fed up enough to do something about it.
Firstly I would recommend getting one of the cheap third party magnetic covers from ebay, that was you aren't messing up something that is quite expensive.
Now to the meat .. put your ipad on your dock and fit the magnetic cover.
Mark on the cover with a pen the edges of the front of the dock, but make sure the cover is aligned properly on the ipad first.
Now get a sharp & strong pair of scissors, cut where you have marked for about 8mm straight up from the bottom edge.
Next angle the scissors inwards from each cut and cut across in a straight line. It's tough cutting but stick with it.
Now re fit the cover to the ipad and place it on the dock, it should all fit nicely, you can now keep your screen clean & protected when your ipad is on the dock.