About using a Portal for ArcGIS Account to Log in to Analytics :

When you configure the ArcGIS Web Adaptor, which is used with Portal for ArcGIS, you must enable both Windows Authentication and Anonymous Authentication (If Anonymous Authentication is disabled, Analytics is unable to log in because, for security reasons, 3rd-party applications like Analytics cannot access content on a user's behalf even if they have the user's access token.

But, if you want to use Integrated Windows Authentication with your portal, you have to disable Anonymous Authentication.

So, it would be nice to keep the Single Sign On strategy if we use Geocortex Analytics ! Why not by modifying the Geocortex Web Adaptor Extensions and/or creating a new Geocortex application pool (eg.: IIS AppPool\GeocortexAnalytics) ?