while this can be true, it can also be a pain in the arse. 90% of the time when I am setting up gears, I toss the old shims out with the bearings. A good installer should know his gears and know the axles he is setting up.
Hell, I just did a D30 the other night. started with an empty housing. nailed the pinion depth of the first try and only had to adjust the backlash one time.
The shop that does things like charge extra for setting up an empty housing, or charges extra for installing a locker or posi. In my book thats a clear sign of a rip off. I've heard of guys/shops that knock out a set of gears in 45 minutes. My best on a D30 TJ wheels up to wheels down was 2 hours 15 minutes with an ARB. a good average is 3-4 hours an axle for most axles. I've setup gears in a naked D44 in like 45 minutes just for the gears setup.
Figure out what the shop is charging, and what they do. How clean do the make the axles? If there just swapping gears and bearings and stuff then its really not taking them that long. figure shop rate times how long they actually take. then let them err on the high side a little cuz it is a specialty task. If a shop charges $100/hr and the guy knocks out each axle in 3 hours, then $300/axle is a fair rate. but these shops charging $500/axle!!! screw that.