My dart race series aluminum heads have been flat milled a lot. The intake valve seat edges have been cut into, but not enough do damage the actual sealing of the valve. This is with a 2.25 intake valve. No PTV clearance issues with a 236/245 630 lift 114 hyd roller. With a flat top JE piston that is

I believe the reason dart gives those specs of maximum flat mill cc's, is for the reasons you mentioned. And why I said some heads can be milled more than others. Not all the same .

On afr's site, on the 325cc head , the chamber is 117 as cast, and 121 CNC ported. Their spec is .006 per cc . maximum flat mill to 108cc for as cast chamber , and 114 for CNC chamber. Angle mill, .009 per cc to 104cc for as cast or CNC chamber.

I'm not trying to start an argument, just wanted to point out one action causes a reaction, mill the heads all you want. At some point you have to cut the valve seats to recess the valves back to where they belong, which changes the installed height of the springs, and may cause the need for new push rods. Angle milling the head surface creates the need to mill the intake surface back to the proper mating angle. There is a point where the intake manifold has to be cut to match the heads.

Sound like more trouble than its worth.