You control the depth of the cut. If you want to be accurate to .001" then do it on a drill press or better yet a mill but I can tell you that the machining from Ford on cylinder heads isn't terribly accurate to begin with.
Don't go trying to measure angles of the rocker arm studs using the bolt holes as a reference. You will be very upset in the findings. Even the center lines of the rocker arm bolt holes are not right on center.
It COULD be why that particular set of heads were left with the bolt down pedestals but had spring height work. Certainly the PC stem seals are the right thing to do.
I never tried to put bigger valves in a 351-C head but have on Windsor heads. The valve guides are so off on them that it's typical that on the same head you can get a 2.02 in two of the combustion chambers but only a 1.94 in the other two.
These things are just production heads designed for lo-po applications and in most cases would never go over 5,000 rpms anyway.
I would expect Cleveland guides to be as inaccurately placed as the Windsors although I have never measured them so can't speak to the commonness of the occurrences?
Even on my factory Boss heads with which I had nothing to do with the cuts, the studs hardly line up perfectly.
As long as you stay with basically with the cutter just kissing the pedestal bolt height, they work fine.
In addition to the cutter, you need a guide so by the time you total up the parts you would be better off paying the shop $150 to $200 to do it for you anyway.
On a mill in the shop, all you are going to do is put straight edges on the pedestals as reference points and use a square to get the cut "plumb".
The cast pedestals didn't need to be highly accurate because of the hydraulic lifters. Solids with guide plates is a little different.
My converted heads worked as well as the factory Boss heads did. So my procedure was accurate enough for a .600 lift solid lifter cam, with guideplates, 7/16" studs and roller rocker arms.
I know from using Jessel shaft mounted rocker arms that you had better be right on it because there is no play in their operation at all. Although typically you have to shim the rocker arm seats for height and they usually come with an assortment of various thickness hardened shims as a result. In other words the manufacturer is aware of the heads being not machined accurately enough.
In fact you might NEED aftermarket heads to use with those? So far for me, the aftermarket heads have been right on the numbers but you really can't tell until you go assemble everything and check. You can't mess around with them at all. Your first indication probably would be to immediately bend all of the push rods at start up? 