John,
The way I understand it ( I'm still sorting this out as well ) you still need to have a base "Tune" loaded in the ECU for your bike that matches up to the changes we are making to the exhaust, intake using TuneEcu Tuneboy etc...
I was not planning on using the auto tune, I was just going to have the bike dyno'd and be done with it.
A couple of things that changed my mind were the people who have auto tune say they are worth it, and my dealer wanted a minimum of $140 up to $200+ to adjust the A/F mixtures. The dealer is also brand new to the triumph line.. so I am not sure of their experience in tuning a rocket. So for a few dollars more I got the Auto Tune.
I have a base TuneEcu tune that goes with the R3T, jardines, triple filters.
The PCV with auto tune and the fuel table that Hans has put together based on Wayne's work... so as Hans told me.... the auto tune will constantly adjust your mixture to give the best efficiency according to the AFR table.
Perhaps someone else that actually knows first hand will jump in and better answer your questions... but that is what I understand and the direction I am heading with my bike.
Curt