Can I license users based on the SharePoint feature sets that they have access to?

Yes –  user SALs can be determined based on the functionalities that they have been authorized to access.

 

E.g. If your end-customer have 100 named users out of which only 20 users require access to Enterprise functionalities and the remaining 80 users need only Standard edition functionalities, you should be able to report this usage as:

 

100 x SharePoint Standard SAL + 20 x SharePoint Enterprise SAL.