Yes, I have had similar findings. For example, when utilizing the Image Server Extension of ArcGIS for Server I was required to re-authorize my server with a new license file that had a code for the image server product/extension. I had to license the rest of my site's GIS servers in the exact same way in order to avoid errors showing up for users and in the AGS log. I makes sense though... your ArcGIS for Server site, if it contains multiple servers, shares the cores across all of the machines. This is part of the whole load-balancing concept. Since ArcGIS for Server is licensed at the CPU core level, you would need all available cores to be licensed... not only on the machine you send the requests to but for all machines in the site. Clustering within the site does not matter, it seems.