The taxman wants all the taxes he can get. *shrug*
Since the FET (Federal Excise Tax, IIRC, 11% on rifles, 12% on handguns) is paid on the firearm based on its value when it leaves the manufacturer, buying a stripped action and then having a gunsmith make several thousand dollars worth of customizations to it "cheats" the ATF out of a significant chunk of taxes that could've been collected (if you'd bought the rifle in its final configuration, rather than having it customized).
Thats why its cheaper to build an AR15 from a stripped reciever and a parts kit than to just buy one, the FET on the lower was only $10-20 vs $70 for the complete rifle.
Of course, the ATF is going pretty far outside the bounds for this, but that is their reasoning behind it.
Kharn