I updated the permissions on the right side (all pages) permissions with a custom role. Gave it almost all permissions. Then I had a user log in and it appears only 1 root page got the role. The remainder root pages don't appear to be impacted by the additional role. Inheritance is set for all the root pages. This is version 6.3.5000.
I may go and 'break inheritance' of all the root pages and add in my custom role, but I'd rather have or hope to have this inherited by the 'all permissions' link on the right side. I would think this was the purpose.