The Auditor General looked at how the billion dollars was spent over 10 years. That information is broken down and shows that more than two-thirds of the money that was spent went to licensing gun owners. The $4.1 million, as far as I'm aware, is a figure that was given by the RCMP when they were asked how much would be saved if the registration of rifles and shotguns were eliminated. Remember, 7 million have already been registered; it's only a few hundred thousand every year that are re-registered, so it makes sense to me.
There was previous testimony by one of the deputy commissioners that put the estimate around $3.3 million, I think. But those figures come from the RCMP, not from the Auditor General, as far as I know.