One is in New York, one is in South Carolina. The reactors in NY are a different type than those in SC, but that has no particular relevance as they are all different from what is used in the fleet. I've heard of some cultural differences. AFAIK, selection just has to do with availability in the pipeline. By the time you get to the point of stating a preference for the Navy to ignore, you will have way more information and scuttlebutt than you will get here.
My information on this subject is 2nd hand.
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