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I believe that ArcGIS Server will use whatever cores are present. In other words, the licensing terms and conditions with regards to the number of cores is not enforced and therefore rely on you to comply with them. I have heard ESRI discuss this at a past Developer Summit and they mentioned that it might be enforced in the future.
The only way that you can comply is to license the number of cores on the machine. If you wish to license less than the number of physical cores then I believe that you have to use a virtual machine where the limit is set in software.