I am trying to visualize exactly what it is you are saying. If the pitting is not covered by the new gasket around the holes, then it is not a problem. It does not need silicone on it. If the pitting is under the gasket material, then the block should be decked smooth and square decked prior to the assembly. If the pitting is so bad that decking the block will not remove it, then I would also consider whether the cylinder walls are still thick enough for a rebuild. Look at the overall block condition, and determine if you want this to be a longterm rebuild, or a stop-gap build. JMO, but I still contend that anything worth doing is worth doing right every time. Joe-JDC.