Annoying PWM sound from Xantrex inverter

Think of a battery sense line as the same as a meter lead. Meter leads are very small wire and yet the meter reads very accurately. This is because there is no current flow. Some better charge controllers use this to sense the realtime battery voltage rather than just pull the voltage reading off of the controller output.

While not ideal, my MPPT controller is connected to the inverter input for convenience. I have the same inverter as you and there is no noise...ever, no matter what stage the controller is in.