From what I have discovered so far. If I tune NA the exhaust would need replacing for much bigger bore. The std air intake is extremely well designed and gives a lot of bottom and midrange grunt. Don't fit airfilters straight onto the throttle bodies you will lose a lot of drive. Combine that with wilder cams and you will lose even more. The throttlebodies are smaller bore than the old bike?? Bu a good combination is still possible provided we get full ecu control. Bob Carpenter did a great job with the old R3 but had to raise the rev limit to 9000rpm to achieve the power goals. My supercharger gave more torque and power without touching the engine, if you went into the engine as well it was down to mechanical strength being the limiting factor to how much power you could achieve. I have tuned the old r3 with supercharger, cams and exhaust and pistons to 380whp but if it was used hard it wouldn't last long. The new engine I think is structurally more sound, but lots of parts are lighter weight so for sure parts will break if you went the same route.
My goal is to change parts to make power efficiently and reliably . the right cams and exhaust will mean better power characteristics without to much boost. To enhance everything that Triumph have produced. So to answer your question, fitting cams and exhaust will give you great gains, certainly pushing 200+hp. Pistons for forced induction are lower compression, NA would be higher compression. So if your final goal is supercharged power, leave them until your ready. Certainly you can make a start.