Grady, thanks for the additional info. I'm using 98mm Mahle pistons and cylinders with 0.002" clearance. I did not have rings on the pistons when I was checking the clearance, but I did torque the heads.
I can see now that machining the pistons would not be a good idea since I could end up with a wider opening at the edge of the piston.
Since the heads were machined 0.008", I'm planning to stack a 0.5mm (the previous size) and a 0.25mm base gasket and recheck the piston to head clearance. I was really trying to avoid stacking gaskets.