Nice thoughts Martin. I'm with you on the natural-holes-lead-to-cup-marks idea. I've been thinking along similar lines, I've noticed that there are often naturally holed stones near cup marked rocks. Fyfield Down is a superb example, what with all the sarsen holes.
I find the crossover twixt natural and manmade, where the line blurs, really appealing too, with phrases like 'artificially enhanced natural feature'. They're such thoroughly threshold phenomena. I love 'em.
I was up at a place this week, where the line between natural and artificial cups is so blurred, even Stan Beckinsall is wary of saying yay or nay.