I installed the new Bitnami version and upgraded the instance this morning. Discourse now runs at the root URL and the broken email and registration links seem to be fixed, along with the notification icon.
I also upgraded the AWS instance.
The only problem was the image asset links were still pointing to the sub-uri but a rewrite directive should fix it for now.
Please post here of any new issues encountered. And thanks to Sam, Jeff, and the Bitnami and Discourse team for their help as well as building some amazing open source forum software!