From my understanding, based on conversations with Steve, one perfect example is taming the delivery of power on initial throttle at low rpm/low gear, in the same manner that a "Throttle Tamer" does with a physically modified pulley on the throttle cables. This prevents the famous C14 "snatchiness" (which really is bad). It is quite effective, I noticed it immediately and have actually considered removing my Throttle Tamer (since now it is a little too corrected). The same type of effect can be had in other areas. I don't know all the details. I know that you can't just cut fuel too much (or adjust spark timing too much) without also limiting air intake due to negative effects (going super lean, possible preignition, etc), and that positioning of the flies to assist is helpful. Steve would be the source to explain what he is doing, if he is willing. I know the results of whatever he is doing is far superior to Guhl flash (which pretty much just slams the flies open and doesn't do anything else with them) based on my comparison of the two flashes (had them both for years). How much of that involves the flies, I don't know.
Weighing in, better late than never.
This is an interesting conversation. Let me explain some things that will make sense. First of all, "performance" in my world doesn't just mean power. Having the same power but increasing economy is also "performance". Some may feel ridability is a measure of performance.
That said, there are some truths here. One is that Ivan's flash won't really be affected by having the flies in or out. Neither would my Hammer flash. Now some history - and this isn't flash war, it's just facts - My flash was out 2 years before his. The theory that I used to tune the secondaries was to open them out of the way enough to allow all the power available at whatever the throttle setting was. Ivan did the same thing. It's an easy approach to tuning. Get the secondaries out of the way, tune fuel, spark, and any other parameters necessary. There is some advantage to throttle sharpness and potential economy by not having the flies open 100% when the primary throttle is open only 10-20-30%, so that was my approach on my very first flash, Which in now The Hammer flash.
Next truth - I released that flash mid 2015, and it wasn't long before the feedback was "I love the power, but I need more engine braking" . Well one of the casualties when the flies are opened alot is engine braking. So I went back to work trying to figure that out. WOW... that was a job. I had a couple interim flashes before getting to the Mountain Runner line. Trust me, I was breaking new ground - I don't know of any tuner anywhere who has done anything like this, because its NOT EASY.
Truth... As BDF stated, the stepper motor isn't quick to react. He's absolutely correct. So when building the Mountain Runner secondary mapping, I had to anticipate throttle action and have the secondaries moving with the throttle. Again, not easy. It cuts a very fine line... open the secondaries to much, lose the engine braking. closed down to much, the helmet banging and excessive factory engine braking is right there to ruin your day.
BTW, this is the reason I decided to bring back my original flash, and offer multiple flashes. Some folks want the engine braking. To others extreme throttle sharpness at light throttle makes them feel that the Hammer flash is stronger. Actually, when comparing the Hammer Flash and the Mountain Runner Premium flash it's a misconception that the Hammer is stronger. The top 50% of throttle on MRP and hammer is the same. The difference is that for light throttle MRP has the really finite throttle control and engine braking that the Hammer does not have.
It still amazes me that anyone who has not experienced the difference that secondary tuning has on the overall personality can even try to quantify it. There are some on this thread who have ridden with flies out, or a flash with flies way open, and then are riding with the Mountain Runner secondary controls. They aren't speculating - THEY are telling us how noticeable the difference is. This isn't sales tactic folks, this is a very real distinction in the personality of the flash, and how your bike responds.
Steve