I think you are all a little right, and all a bit wrong too. .001 inch isn't at all dangerous. I'll bet that there is more variation in barrel diameter over the length of the barrel than that. I'm sure that Beretta is as lawsuit-shy as any other company in this litigious society and would naturally advise not to shoot the gun. Mild gun barrel steel will work harden and that is not a good thing in barrel steel. Taken to extreme, work-hardened steel in a single spot on a barrel wall is a recipe for catastrop failure if subjected to sufficient pressure. Non-hardened steel barrel walls would probably just bulge. But in my opinion the cold work to take out .001 isn't going to increase the hardness of the spot to such a degree that there is any risk to anyone.
