It's just a reference really - from the case base to the bullet ogive. The true COAL is from the base to the bullet tip but because bullet tips can vary, measurements can vary and therefore the measurements are unreliable. Using the comparator is a more accurate way to measure an OAL and that number or reference is useful when you're adjusting seating depth. Bullet base to ogive dimensions can vary as well though, even within the same lot, depending on bullet manufactures. I've found Berger much more consistent than Sierra, for example. The comparator's most useful function is to sort bullets by their base to ogive length. Once you have a batch of sorted bullets and have chosen a seating depth, you can be assured seating depth relative to the rifling will be the same, which is important. Or at least within the tolerance you sorted your bullets to.
How you set your calipers up really doesn't matter. Either zero them with the comparator installed, or not. In the end the measurement can be used in the same way.
