I've read that Cannondale sized from the top of the BB to the top of the seat tube.
So it was seat tube length
C-T is usually to the top of the top tube join on the seat tube.
C-C would have made the frame a little bigger with the large diameter tube, and the long seat tube neck above the top tube could have thrown people off even worse.
Seems to work, and explained to me why they always seemed to be a little smaller than expected.