Kent,
The "all gear" method can be a tuning tool also. Lots of good information on that run sheet that can be very beneficial with proper interpertation.
The two run method "all gear" and roll-on can be used together to not only setup and tune the engine but also look at potential issues with the lower end, tranny and the drive train that might not, yet, be obvious or evident to the naked eye.
If the bike is tested properly every spike and dip on the sheet will tell you something about the engine and drive train.
Buzz