Nikon France representative said that the added thickness of the sensor cleaning module explains the 95% coverage, not the built-in flash. See my post here.
I agree that the 95% viewfinder thing is not an issue & like the sensor cleaning feature on my D300. I rather use it as much as possible than create a hurricane in the sensor chamber with a rocket blower that sends the dust who nows where! It gets rid of the dust on the sensor 95% of the time.