I'd say yes, it will decrease the value (definitely won't increase the value), because most people will see it as a "he's trying to fool us into thinking he has an R or a Tricolore" effort vs. "he just really likes the aesthetics." Kind of like putting an M3 badge on a 3 series....not as shameless, but kind of in the same ballpark.
If you're going to go through all the trouble (and expense) of turning your base into an R-or Tri-looking bike, you might just want to consider going balls-to-the-wall and get a full on RR Carbon fairing kit from Bellissimoto.
BellissiMoto - CarbonVani Carbon Fiber parts for the 1199 Panigale
Or come up with something unique and tasteful that WILL appeal to someone come time of resale, who thinks, "damn, I LOVE that paint scheme."
Great to see someone in Alaska rocking an 1199!