Glad to see you stick to your guns, bluelab!
The Thunderheader is absolutely a much better performer in high output engines and can, and will, cause a torque dip on mild or stock engines because of overscavenging; especially on the front cylinder. With all due respect to Ozzie, Chuck, and Bella Lagosi, the pipe is NOT a drag pipe but your tuner has legitimate concerns IF he doesn't know how to cure the problems. The stock cam simply does not have enough lift and duration to allow the TH to do it's thing and your EFI system will have problems dumping enough fuel into the cylinders to compensate for the TH high scavenge rate. Stock heads also greatly limit the ability of the TH to perform. However you will see gains due to the combination of the AC AND the TH, although your bottom end will see little to none, and you high end the same as the bike will simply run out of breath as the TH will be sucking on a closed straw. So midrange is left and that is where you ride so there will be gains. What you need is to address the basic cam and head issues and you will already have a nice exhaust set up in place. The TH is a great pipe (top 3 or 4 IMHO) for performance, but you don't have the performance combo yet. And I have been saying this for years, if a tuner doesn't know the inherent issues that come with that pipe and how to tune for them, especially on a stock build, then your gains are small. Great loss of power in the bottom end?? No! You won't feel it on a stock bike, anyway. But no big gains either! The pipe can be adjusted with both separate cylinder AFR trim and timing AND working the tabs in the baffle to cut down on the scavenging rate. If your tuner doesn't know how to do that (or doesn't want to) then find another tuner, regardless of what pipes you go with.
(Every time Ozzie is on the same thread I tend to write a short story. Now my head hurts!!)