Fitting questions - Effective top tube vs horizontal
If you look at the full resolution it is clear. 
BS is center to center (head to seat) along the (sloped) top tube. 
Since the seat tube is slanted that is a shorter distance.
Geomemtry C2C

Cathetus and hypotenuse apply to a right (90 degree) triangle.  There is not a 90 degree triangle on the BS.