Named user licensing works for spreading the cost burden on public AGO implentations using ESRI hardware and software. However, organizations hosting Portal internally with their own software hardware and data should not be bound to per user licensing models. Furthermore, tying access to portal licenses to the number of concurrent ArcGIS Desktop linceses makes no sense as the entire point of concurrent user licensing is to allow a pool of users to use a finite number of Desktop seats. Per user licensing is also not helpful in the respect of account management as access must be reassigned as emplopyees come and go.
Either implement a license model that replicates a concurrent user license pool, or drop named user licensing for internal Portal implementations altogether.