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What you are describing is the best method. Holes should be easy enough, and can actually be recognized (if using recognition that is) in your global setup if you would like. Copying and pasting is actually a great solution, so long as the setup is in the same relative location for each part. As you mentioned, this could get a bit spicy with complex parts.
I'd say this is particularly helpful when doing production runs. Just do the quick mental math on a project as to whether you'd be better off spending some extra time on the front end really dialing it in, or if it's just better to do the hand programming subroutine method.
I have seen a development request for multi-axis functionality in .mf documents. I think this would really get to the heart of this issue, and many more. I'm going to go ahead and add this thread to that internal development task. Just for your records, that task is FCAM-2667.

Kelbie Ockey
Sr. Implementation Consultant