Well he's kinda right, and kinda wrong. Not only is the tune different, but the tables within the tune are different. What that means is its not as simple as loading a Standard/Classic tune into the R3T, it flat won't work.
Now, the only tune your dealer will have available to you is the TORS tune. Which of course requires a set of TORS mufflers. That change will net you something in the neighborhood of 10-15 horsepower, nowhere near covering the deficit.
If you really want similar horsepower to the Standard/Classic models you will need to change out the exhaust, Jardines at a minimum and strap on a set of K&N filters. Once you've done that you will need a custom tune via either Tuneboy or the newly released TuneECU.
So add in the cost of the exhaust and filters along with dyno time to tune your bike and you're talking about a decent investment. It can be done, but its not nearly as simple as your dealer makes it sound.