NOS,
The only thing I can see that pops out is when you are taking the seat to center of bottom bracket measurement the height of the bottom bracket from the ground would have to be the same on every bike I would think. If a bottom bracket of a bike is higher or lower than the custom bike this difference has to be considered in making all the measurements the same. The different heights if they exist would also change the angles of the head tube and the down tube wouldn't they? I think this would make a difference. Maybe so, maybe not.

As said above, you can over engineer these points too. (This coming from a man with engineers disease really bad.)

Bill