For me, its the intentional vs unintentional. You're probably correct, it will displace the burr and be fine. However, If I'm doing it, I'm going to apply the dimpling evenly to make sure there isn't any change of the displaced material "biasing" the fit of the joint. In fact, if it were mine, I would clean up the raised material and then dimple the ball joint if I needed too. That's just me though...I've never been the most efficient mechanic.
The ball joint will easily win this battle with zero detriment. There is zero chance of that little burr hurting the fit.
