You pose a good question about the 2015/2016 model. I don't believe it will matter if it is a 2010-2014 or 2015-2016 with an ECU flash, but I don't know for sure and would not be the right person to answer that question.
Changing the air filter or the muffler will do essentially nothing to affect reflashing or PC [performance]. This isn't the 50's/60's/70's/80's.... the Concours' muffler and 2-way cats are not much restriction. I don't believe the stock air filter offers much resistance either. If you are keeping the stock intake headers, exhaust headers, and stock piping, those will be your set restriction points (along with perhaps the throttle bodies... they are slightly larger on the ZX11).
They might have recourse against you if tampering with the equipment does cause problems or failures, but generally they have to PROVE that it caused the problem. Reflashing just updates some tables, it doesn't do anything else that would affect other systems. "Piggybacking" with a PC does essentially the same thing- it doesn't modify the tables, but it modifies the outputs (and/or inputs). It is no less or more "safe" (although is some ways, it is less reliable, since there are physical connections and extra components to fail).
There is no O2 sensor on the USA model, unless something changed that I am not aware of...