CBR954,
think you fundamentally misunderstand the function of the tools used. What is "surface prep" other than removing material??? If you produce a cross hatch pattern in a surface, you remove material, how else would you see the pattern? Even if you 'only' polish/buff a surface, you remove material.
And the step in the ring zone will not go away, cause the tool follows the cylinder wall shape. That's why you cannot correct a worn bore by honing, 'deglazing', whatever you want to call it. And 5 thousands of a millimeter are removed very easy. Did you interpret my numbers in inches? Sorry for not adding the mm, but it's a metric bike, so I automatically think in millimeter.
Just a reminder: The recommended piston clearance is only 0.02mm, maybe 0.03mm. If you remove 0.005mm by , you increase the clearance by 15-20%.