I know this is an old thread, but just so you guys know what you're looking at if you think the machinist made that mark, it's called an inclusion, it's a flaw from the casting process where sand breaks off the mold and falls into the molten aluminum. Turn enough cast iron on a lathe and you learn pretty quickly how to identify these things.
Anyway, if you run across something like this in the future inside the combustion chamber, take a dremel sander or some paper and just smooth it out. This will keep the edges of the inclusion from becoming a hot spot leading to detonation, and will lessen the likelihood of the pit becoming a stress riser for cracks. A rough surface in this environment will also invite deposits.
If the inclusion is on a mating surface how you deal with it will depend on how important the seal is, how much stress the seal will be under and how much risk you're willing to take.