Need Advice on Machining the Intake Surface of the Head (gasket crush)

why use spacers and clay, makes no sense, oh hughes said to? If u want to see what the actual gap is use just clay. your average top gap is .052", average bottom is .058" - with spacers artificially holding the intake away from the heads
The only things you can really measure with clay is the RELATIVE gaps top-to-bottom with the intake undistorted by the intake bolts. The washers just make the numbers more consistent side to side and easier to interpret and to visualize in the actual installation IMHO.

However the relative gaps top-to-bottom will be the same with the washers or without. You could use washers half the thickness or just clay (no washers at all) and get the same RELATIVE top-to-bottom gap measurements.

U r measuring an uncrushed new gasket? I cut my heads .017", and like a good squeeze on the intake gaskets, did not cut the intake faces.
As long as the intake bolts are not hitting against the upper edges of the holes in the intake as torque increases (and thus limiting the intake's movement downward), then the crush for a given bolt torque does not change with the heads cut or not. But IMHO it is wiser to do as above and start the intake 'riding high' a bit as you try to start the bolts.