The controller will determine how much power the battery bank will receive based on its charging algorithm and battery condition.
Based on the above information, the controller will then adjust its input port impedance to consume enough power to cover its internal losses and the power delivered to the battery bank.
This means the controllers input voltage will vary, typically on the high side, to ensure the panel delivers required power without excessive losses.
You must remember that the panel acts as a constant current source until the voltage approaches its open circuit value and then the current falls off quickly.
So losses in the wiring between the MPPT controller and higher voltage panels have almost no effect on the charging stage unless the batteries are severely discharged and the panels are operating at their maximum power levels.