K&N or Ramair under the stock claw have ZERO issues in the rain, I speak from 2 years riding in Hawaii, it RAINS here sometimes, and I ride in it. Bikes sat outside the office all day getting dumped on, and zero water issues when I go to start it.
As for the tune... Your dealer is making the typical "ignorant dealership" comment, they don't know what TuneECU or Tuneboy are clearly. You dont "need" a PC-3/V for the air intake/exhaust tune, but it allows anyone with a dyno to tune the bike instead of trying to find a TuneECU/boy specialist.