You probably ought to talk to Brian or a good tuner to find out why things are the way they are. That is exactly what a power commander or a Bazzaz QF does - more granularly than just the ECU. If you look at it in "steps" or "cells" that can be adjusted, the ECU is typically more limited by itself (flash or no flash) than a PC or Bazazz. Any good tuner is going to charge you the same for a tune on the dyno as a baseline (there are slight cost differences for example between some guys tuning PC vs Bazzaz, as the Dynojet software saves them some time when they're tuning with PC vs Bazazz). Brian can get you more in terms if A/F and ignition timing if you have a PC/Bazazz vs just the ECU. So, IMHO any good tuner is going to recommend you make max utilization of the money you're spending. I'm not sure who's writing that a flashed ECU is making more power and better response than a properly dyno tuned bike. Frankly, again IMHO either they're making crap up, or they're comparing it to an ineffective tuner - period. No other option.
None of the good tuners I know will flash an ECU without it being on a dyno. Doesn't mean none will, just none I know. Tuners dealing mainly with street riders are way different. Street riders are far less concerned about throttle response than guys on the track. To me that's more important than a hp or 2. That's why generic maps for Bazzaz and PC are far more popular on the street. When you think about the cost of every race or track day, cost of tires, safety equipment, fuel, suspension, rearsets, clipons, bodywork and paint........ the cost of a PC as a one time investment is less than nothing.
There is NO "median" for true performance. Every R6 will have very slight differences that require small deviations. Valve lash, ring seal, air cleaner, tiny differences in how much carbon is on top of each piston, all kinds of minute variationsOverall curves will be very similar, but good tuners don't do "similar". They do "optimal" because that's what guys are paying for. A generic flash may be fine for you, like I said - it all depends on what you're looking for. Good luck with whatever route you go.