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.
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.