I didn't do a before and after dyno test because that would have been both expensive and inconvenient. My initial motivation was to get rid of the standard headers as the valve had seized. I decided on the Akra headers in stainless - more robust than titanium - and then went the whole hog with a servo buddy and Hilltop remap. It doesn't really need the servo emulator but they're not expensive and it avoids having an exposed connector where it is bound to corrode.
The bike doesn't just feel better, it is materially faster. It pulls from below 2,000rpm and the acceleration in 6th at 50/60mph is stronger, less need to change down. The surprise is that it is much more economical unless you are caning it. I got high 40s riding from London to Leicester and mid-50s going home. It delivered 65mpg on a recent road trip with a mix of motorway and A-roads. I'm going on a trip soon with a mate with a new R1300GS, it will be interesting to swap bikes and do a direct comparison. I rode a 1300 in Romania and it felt no faster than my 1200 and was less happy trickling through town at 2,000rpm.
I have had lots of GS's and I have had other bikes remapped too. This remap was the best I have ever experienced.
Regarding the advice from your race engine company, that sounds very....odd. Removing the cat and valve, and adding larger diameter headers with better gasflow will do much more than changing the silencer. And removing the O2 sensors means that the ECU has no way of knowing how the engine is running.