You could measure it anywhere as long as your consistent. Most will go with the point that is equal with the fadeout. Figuring in your taper rate per inch you then calculate what the stack is/should be at the butts. However, many thickness sanders will rip away more material at the beginning of the feed so getting reliable numbers very close to the butt of a lamination can be more pain than its worth.
Interesting note: Binghams tapers will very often be parallel for up to 8 inches of the butt end. Then after the 6-8 inches they start to taper. This makes it impossible to use the butt thickness as any sort of indicator of final stack height.