Hi Stephen, a couple of months ago i had the same questions, and testing got this:
- First, when you use anonymous acces in your portal the users can go and use the map tool and access to layers in groups that are public and with public content (in other words shared with "All" and "my organization"), if is not public content and public groups they cant access to that content, they can't add new layers to the map.
- Anonymous access for users it does not have to do with ArcGIS web adaptor, what the option in web adaptor config means is a anonymous administration for ArcGIS Server.
-Anonymous access does not have to affect your licenses, one license spent only when you register a user, with anonymous access the users do not require to login, i recommend you disable the default page to register users, then they can't be registered by they self.
I hope this can help you.
Regards.