If his heads have a .060 recess cut in them, the piston needs to be out of the deck.
As for killing flow, you'd have to spend some time on a flow bench. It damn sure does affect flow. Think about how important a top cut is. Then you move the deck closer to the top cut? Bad idea. You can mill a head within reason. To run a zero deck and then deck the piss out of the heads to get the CR you want is *** backwards.