I'm a aerospace machinist, of over 50 yrs experience. You can't use a end mill to spot face or counter bore a area, unless you can interpolate that area, with a smaller end mill.
End mills have a end cutting relief of 3 to as much as 7°. Meaning that the center of the cut, will be higher than the outside edge.
A c'bore or spot facing cutter could be used, by hand, IF the pilot is is very close fitting, say .002, and fairly light pressure used, so that you don't push it off to the side, while applying pressure.
All the above, is based on the hole, for the cross bolts has been done accurately in a milling machine.