Your right, unless you buy a set of gears without the original shim and your starting with an empty case to build. That is what I always liked about Dana gears. They have a number either positive or negative that gives you a starting point when selecting a shim.
Yeah, I get what your saying, I know aftermarket gears like Richmond have the pinion depth marked on them, but it would be a pain to get that right unless you had a "set up" bearing for the pinion, that was slip fit...