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It very much depends on industry. Large-scale (aircraft, shipping etc) the holes are not shown as circles but represented by a centerline symbol only (which may be a simple two-line cross or something more sophisticated with letter/number codes in one or more of the quadrants). In that case, the arrow head of the balloon will be close to the symbol but not touching anything.
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not covered by standards is a surprising situation?
My preference would be the edge of the hole same as rad. and dia. dimensions. Perhaps the drilled dia. for tapped holes.This way you can see the arcs/circles are associated with the hole. However as Chris points out, we actually machine to centres.
Answer, give users a choice.