I don't want to combine desktop licenses with pro licenses on the license server.
i would prefer they stay separate.
Yes. ArcGIS Pro CU licenses will be different from ArcGIS Desktop (ArcMap) licenses, even though both can be hosted from the same ArcGIS License Manager.
For more details, read Concurrent Use licenses—ArcGIS Pro | ArcGIS Desktop
You must install ArcGIS License Manager 10.5.1 or later to manage ArcGIS Pro 2.0 Concurrent Use licenses.
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