The Netcentrics GTD Outlook Add-In will automatically configure Outlook in the way we suggest in the Setup Guide and then give you a toolbar to automate some functions and views for seeing things like Actions by Project.
So it does some of the same in terms of initial setup, but then gives additional functionality that "vanilla" Outlook doesn't provide.
That said, we typically recommend people for the Add-in when you have a solid understanding of GTD. If you don't yet, I'd say stick with the Setup Guide and vanilla Outlook for now.
Hope that helps!