Those are chatter marks. They happened, then the chrome was applied over it. It's not really something you can fix. If you cut more to make it smoother, you'll loose the chrome there (which creates flaking later) plus that would make it bigger. It's already oversize where it chattered. A 9mm chamber reamer won't cut any larger than spec dimension, so to cut at all you'd be using the wrong tool. Bad juju all around.
As far as what it causes negatively... nothing until the chamber/gun gets extremely dirty. Then it will cause a decrease in reliability, due to increased fiction/resistance to extracting. You'll encounter this soonest with weaker-loaded ammo, assuming an equal level of dirtyness.
If I were you, I'd gripe to Beretta explaining this is a big problem for you, in the hope they replace your barrel for free. They'll likely try to downplay it, and that's after you get them to acknowledge it exists. The pics will prove that fine. Be firm, but not a total d. If they don't replace, it may not really be a big problem. You're talking field conditions of killing zombies for days before the reliability bug bites. Now I understand that may apply...
If so, raid or trade for some +P, keep calm, and fire on!