If you made Z be the distance from the bottom bracket to the hip scoket, your formulas make sense. Measuring to the spindle doesn't make sense since it would depend on where in the cycle you were.

Whenever I see seat angle discussed, it is usually the angle formed by the line from the top center of the saddle to the bottom bracket and a horizontal line. You could argue that it would make more sense to measure it to a fixed point on the rider, but that is tough to measure. Two guys could ride the same bike and you would say one had a seat angle of 78, while the other had a seat angle of 80. That would be confusing.