Been through this a few times with replacement manifolds on older trucks, and the short answer is a divot that doesn't go through is usally fine. Cast parts come out of the mold with little pits and dings all the time, and manufacturers only care about through-holes and cracks.
Here's how I verify one. Take a straight pick or even a stiff piece of wire and press it into the spot. If it stops, it's just a surface flaw, clean it up with a wire brush and move on. Then hold a bright flashlight behind the runner in a dark garage and look from the other side. Any real hole will show light imediately. Also run your eyes along the flange edges and between the runners, since that's where cracks like to hide on these parts. If it does go through, don't try to seal it with anything, just return it. A pinhole will only get worse with heat cycles and you'll be chasing an exhaust tick for months wondering where it came from. One more thing, check the mating surface of the flange for warpage with a straightedge while you've got it out. Cheap to do now, annoying to do after everything's torqued down.