The reference point is the center of the guage on your seatpost (saddle) clamp. The one that you use along with the guage on the rails of your saddle to adjust your fore/aft position.
I checked out your bike (very nice!) and quite honestly, I'm not sure how to judge the sloping top tube and compact geometry for this application. But it appears you have a standard seatpost, (as opposed to a setback) so the idea of moving your saddle back in order to increase overall reach (rather than changing stems) is plausible. It would however, disturb your KOPS setting if your into that.
That said, I'd be interested to know what is the correct way to measure a compact frame for effective top tube length and until this is clarified, I'd suggest waiting before making any adjustments. Does the Wrenchscience website adress compacts?