When flycutting the head, you are effectively reducing the size of the combustion chamber. To do it your way, you are going to have serious issues with the deck height. You would not have to use a shim in any circumstance where you are simply removing material from the base of the cylinder, you just can't take that much off before the piston comes out of the top of the cly. Then you'd have to put a cyl shim in to correct the deck. What does that achieve?
Most people reomove the head gasket and add that thickness to the bottom of the cly rather than lowering the cly. Of course, you can adjust the compression, or more importantly, the squish (the clearance between the top of the piston at the edge and the flat area of the head) with different base shims.
By doing a clean-up flycut on the heads, trueing the top and bot of the cly, eliminating the head gasket and narrowing the squish to .045, you might pick up a point in CR, i.e., 7.6:1 to 8.6:1
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