Generally decel popping or backfiring is from a too lean condition when the throttle is closed at say, 3500 RPM, but not always. Barring any exhaust leaks, I'd guess that the bike has probably always run that way. If I had a slight pop or three when the bike is not fully warmed up, I wouldn't be too concerned, if it all but disappeared once the bike got up to full operating temperature. But if it's doing it all the time, I would not be a happy camper, as it should not be doing it.
The dealer (the bike is still under warranty) should check for exhaust leaks and eliminate that possibility. Beyond that, you're going to have to discuss with the dealer why they would suggest an exhaust system and whatever download they might/might not have done that makes the bike run so poorly. And decel popping is NOT normal, so don't let them use that one on you.