If ATF has always considered such firearms as rifles, there would be no need to issue this rule that redefines "rifle".
But the ATF didn't redefine "rifle," they "clarified."
This final rule’s amended definition of “rifle” clarifies that the term “designed, redesigned, made or remade, and intended to be fired from the shoulder” includes a weapon that is equipped with an accessory, component, or other rearward attachment (e.g., a “stabilizing brace”) that provides surface area that allows the weapon to be fired from the shoulder, provided that other factors, as listed in the rule, indicate that the weapon is designed, made, and intended to be fired from the shoulder. (Page 269 of the final rule.)
Again, I quoted the exact wording of the final rule, and that wording shows up four times in the final rule, under "Current Unlicensed Possessors" (page 271,) under "Federal Firearms Licensed Manufacturers or Importers under GCA and Qualified as an SOT (Class 1 Importer and Class 2 Manufacturer) Under the NFA" (page 272,) under "Federal Firearms Licensees Not Having Paid SOT as a Class 1 Importer or Class 2 Manufacturer under the NFA" (page 274) and under "Certain Governmental Entities" (page 276.)
So I think they are serious about how they see the status of these firearms. If it was delivered with a brace, it is a rifle, but you have 120 days to remove the brace if desired to make a pistol, and the ATF won't require registration of the resulting firearm as a "weapon made from a rifle."
Just because you as an FFL transferred the firearm as a pistol with a brace, in good faith, doesn't mean that the ATF agrees that you properly transferred the firearm, or that the manufacturer properly manufactured the firearm.
But I suppose those were cans of worms that the ATF didn't want to open...