NSEU is right. The tuner presents the transceiver with a matched load ie 50 ohms where it is designed to operate efficiently.
In effect the tuner makes the antenna look like the right length for the frequency your are transmitting on.
In aircraft the antenna is generally very very short for the wavelength so the tuner has some work to do to make it "look" longer.
They are a compromise, a short inefficient antenna but it is aerodynamic.So they pump in hundreds of watts and tune the blazes out of it to make it work.
As for your over modulation.Sounds a bit odd , aero mics generally need to be close talked to work well so that they dont pick up all the cr@p from the motors etc. Maybe the gain is a little hi on your headset? You shouldnt need to talk really quietly to make yourself readable.
Can you try another headset / mic perhaps?
As for bits moving.It all happens inside the tuner / coupler .(another word same thing).Some have little motors driving coils slugs and capacitors to make the antenna look resonant.More modern ones switch/tune very quickly. The antenna is just a fixed length bit of leading edge/cavity or wire in your case on light aircraft.
Have a read about tuned circuits, antenna theory, and resonance.