BikeCAD defines saddle height as the direct distance from the center of the bottom bracket to the reference point on the saddle. The reference point is by default the deepest part of the saddle, where it may dip down in the middle. However, this point can be changed according to the instructions here.
This dimension will tend to be roughly parallel to the seat tube, but it will not always be exactly parallel. As the saddle is slid back and forth on its rails, the saddle height dimension will shift to follow the saddle. The saddle height dimension will also shift as the seatpost setback is changed.
As the fore and aft position of the saddle is changed, and as the seatpost setback is changed, BikeCAD will adjust the length of exposed seatpost so that the actual saddle height will remain as specified.
Saddle height can be directly input into BikeCAD. Alternatively, the saddle can be located by XY coordinates with respect to the bottom bracket. This is explained at: bikecad.ca/saddle_position.