Yes, a rubber flap cover/plug similar to the one in the below picture would be perfect.
Attachment 65530
I know of at least 3 cars where this distance is a problem. If more, it will hit the climate control unit and 2DIN wont fit. But as long it is within 2-4 mm of a 2DIN unit spec, it should be alright.
That's a good feature. However, if the level of dimming can be configured through the menu, it would be great but even otherwise, it is a well thought out addition.. Thanks Ken Homma!
BTW, the Engineering Sample looks really nice!
Regarding the reachability to the screen edges, its not a major problem since most well designed CarPC front-ends have good sized button and they are usually away from the edges. You could include a capacitive touch stylus for purists though but I guess its use would be very limited in a car except when setting up.