In some cases, the factory-finish is distinguishable on the deck. A dial indicator is normally used, attached to tool that will straddle the center of the cylinder. A machined piece of steel (1/2" square will work), centered over the wrist-pin can be positioned on the deck, then measure the movement of the steel as you roll the motor past top dead center. Obviously, the still will move the dial indicator if any piston pop-out exists. It is legal to scrape carbon before measuring. Allowable is up to .005 pop-out. A bit of advise: Far bigger opportunities in gains though chassis tuning exist, so remaining a few thousandths of an inch under the max pop-out is my suggestion.
Good advice. Be sure to check for angle decking or peak decking as well. You might well have less than .005" pop-up but have the deck cut hard. It doesn't help the flow like it does on the old flatheads, but it does change the valve geometry a bit -- that might be the reason some do this.

Thanks and God bless,
Brian Carlson
Carlson Racing Engines
Vector Cuts