Here's the deal.....
There have been a lot of reports that the Closed Loop EFI's can make adjustments for minor modifications to the intake and exhaust. And that is absolutely TRUE. However, without a way of measuring your Air/Fuel Ratio, you just have the "seat of the pants" to go by.
Hesitation, Popping, Spitting, Stalling, Heat, Header pipe glow, Reading spark plugs, etc.
Since I'm most familiar with the Older OPEN LOOP EFI set up, I can tell you that the Maps for the Screamin Eagle Pipes are different between the Screamin' eagle Swoop pipes and the 16ga Screamin Eagle pipes.
So even with the same air filter, and same headers and same 2-1 third volume, the MAPs is markedly different.
Now, the CLOSED LOOP ECM can compensate, but how much they can compensate is a point of debate. The closed loop ECM is on the bikes for one reason: Emissions. The target AFR for the partial throttle cruising and for idle is 14.6:1.
That's stoichometric. That's as CLEAN as the engine wll run. It's also HOT. An engine running at that AFR is markedly hotter running than one tuned more rich. I really wouldn't care if that engine is behind an insulated firewall. However, on a motorcycle, you don't have that luxury.
So even if the ECM can compensate for your pipe change (and I personally wonder if it truly CAN) do you want it to? At best, you'll still be running at that same HOT engine temp between your legs. At WORSE, you'll be running lean and possibly burning up your exhaust valves.
Here's the test: Have the wrench you speak of put the warranty on the line. Have him PUT IT IN WRITING. Ask the Service Manager if he will honor the warranty on the engine, specifically heat related failures (Piston Ring and valve issues) if you follow the advice given my HIS tech.
Let me know how that turns out.