Here's the thing about the RPM slice of this that confuses me.
1. I have an RS. I use it as a daily driver, in the city. The high RPM is never an issue, because that just means I don't upshift higher than I need to be, i.e. in stop-and-go I ride in first, second, and when I'm lucky, third gear.
Basically, traffic makes absolutely no difference to the Spyder, you just ride it in the lower gears. So what if it's louder? Big whup, I wear a helmet and ear plugs.
2. IIRC, a dealer can hook up the bike to BUDS and see the RPM history, so they know where we shift our bikes. (I've seen earlier threads on this subject). Based only on the above, it sounds to me like the OP's dealer did just that, and saw that the OP was shifting below the recommended levels, i.e. lugging the engine.
Now, that may be a subjective conclusion from the dealer-- is there a technical, BRP-defined definition of HOW MUCH lugging of the engine is enough to void a warranty, I don't know? If not, the dealer could be using this an excuse for poor setup/poor diagnostics. But I guarantee that there exists SOME point where the dealer and/or manufacturer can say, "The rider consistently kept the RPMs too low for too long and inflicted the damage him/herself."
Anyway, without more information, I'm not blaming the OP, and like all Spyderlovers, I wish them all the best. But I must admit this wouldn't be the first time where a rider, either through dealer-induced ignorance or their own error, rode the Spyder at too-low an RPM.
Not including the OP in this category, but my head has smacked more than once from reading the number of Spyder owners who insist, absolutely insist, on riding a high-RPM, low-torque motorcycle as if it was a low-RPM, high-torque motorcycle. :banghead: Ummm, people, the Spyder is NOT a Harley, and no amount of upshifting to higher gears is going to convince our French-Canadian friend that it's a product of Wisconsin.