Tuner said leave 2nd flys in?

I had my bike dyno tuned a few weeks ago. It really hauls now. I took the 2nd flys and shafts out this winter since it seemed universally accepted as the thing to do. However my tuner said that he could have actually made a little more low and mid range and made the bike a little smoother if I had left them in. He said taking them out removed his ability to create better air velocity and turbulence at lower throttle openings. This does make sense to me. I'm not really in a position to tell since the pre custom map was the akra smoothend map with the flys set at 100% all the time. I do know the smoothed map was a ton better than stock. He did say it was a small difference and probably not worth reinstalling the secondary flys. Just curious if anybody else has heard this?

John @ TrackElectronics says exactly the same. Engine with properly tuned 2nd flies is better than one without them.

My '07 SD has all the mods, @nd gear mod, Motohooligan box, Power commander, custom map, full Akra system, no SAS, RC8 velocity stacks but I have kept the secondary flies - although I have the elliptical Motohooligan ones fitted. My map is smooth and this is the most BHP and torque I can get out of this engine now I think.

I haven't plugged TuneECU or PC3 in for so long I can't even remember if you can tune the 2nd flies with a PC3? I know you can with TuneECU.