I actually wouldn't say you were wrong. Stock, timing is less at part throttle, lower rpms. Call it less, call it a restriction, whatever ...
You and I had the discussion some time back about the effect of the "TRE" flash characteristics. I don't see any improvement in 1/4 mile times because I don't use that part of the map.
At the end of the day, lots of guys like the modified timing after the flash.
Oh, another thing. My buddy bought a Busa and we discovered the flies are out of it. These Busas are so consistent that we can make direct comparisons of one to the other, adjusting expected performance for weight, DA, gearing, 60' and the like. His bike performs exactly as we would expect a Busa to perform with the flies in. Again, we really aren't using the low throttle, low rpm portion of the map. Conclusion - not worth doing.
