The output shaft is the tailshaft, that is the correct term to describe it output, it surely isn't the input shaft.
The right way to measure it is if the slip yoke is there that is going to be used, always use that bottomed out then there can be no mistakes with trans that have other issues of internal designs on the output shafts, if no slip yoke is present then the output shaft and the seal location to center or face.
Many shops don't do this and this is why mistakes happen with output shafts that have o-ring issues.