The protrusion is obviously measured from the base of the clitoris, which would generally the the body. Literally just the extended distance from tip top of the clit-clot to the biddiliy bodily.
Barring other random physical abnormalities that would exacerbate the protrusion (maybe an overly developed pelvic humperdoodle)
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Are innies a negative protrusion?
From a literally perspective, yes. And thus the people uncomfortable with a large clit should then be way more likely to lick an innie.