I think a lot of people who don't know better think chris chance built a lot more bikes than he really did just because his sig is on the chainstay. The ebay auctions always crack me up when they say "built by chris chance himself...." Now really early fats and CC roadies may very well have been built by him, but in the glory years fat was a pretty big shop (by small shop standards) and I'm sure they had full time machinists, tackers, welders, and finishers.
Ultimately it doesn't make much difference in the riding. And if anything later ones are probably spec'd a little better. I know at some point they went to the 10th style tubing on most of the yos, which would have been a little lighter. As they grew the demand for true temper tubing it probably got better as well.
As for craftsmanship, well, any handmade frame is going to show a fair amount of variation from one piece to the next, even if the same guy is melting the metal. So you really have to look at them on an individual basis to know if you got a great one or a just good one.
My buck has a mass serial number but a saratoga badge. Chances are it was built pre move and painted post move, but I can't say for certain. Honestly I couldn't care less. It rides great and that is all that matters to me.