This may seem a stupid question but does an admin need to assign a Pro Named User License to the same user both in AGOL and in Portal? It would seem like it then uses up 2 Pro licenses for the same user or can a user just be assigned a license in one or the other- agol or Portal and still be able to access content from both?
ArcGIS Pro, Portal, and ArcGIS Online user account licensing is one in the same. You authenticate the user using the license from ArcGIS Online. Below is a link to more information about the license model.