Custom Pushrods / Preload

You're correct, although technically excessive milling means you need to replace the pushrods with shorter pushrods so the plunger isn't "pushed in" so far giving too much lifter preload. As the lifter is already absorbing a tiny amount of lift just doing it's job, a change like that would be almost immaterial.
What you're talking about has nothing to do with what is considered valvetrain geometry tho. Valvetrain geometry is bascially the motion of the rocker and it's interaction with the valve tip and as I said, cut all you want. Unless you sink the valves, use longer ones or don't trim the stems as part of the valve job, or raise or lower the centerline of the rocker shaft, you will not change the valvetrain geometry.
What you're actually talking about with the pushrod length is affecting "pushrod angle". That's the difference in angles between the lifter centerline and the rocker's pushrod seat's centerline. Not to be confused with "lifter angle" which is pre-set when the block was designed and not very adjustable.