I agree with "DOUGMCP" and his statement "There is no real advantage going to 2ga over 4ga unless you are planning some real aggressive power upgrades." However, for "aggressive power upgrades", you will would want all to be 2ga. For the power upgrades that would be that "aggressive" you probably would be bypassing/removing that controller anyway.
By using 4ga for that one cable, it would be a little more "resistive" than the others but you would still benefit with less total resistance of the circuit, than using all 4ga and for sure than keeping all 6ga.
Just as an example:
Assume current draw is 100AMPs continuous.
Assume total battery voltage is 50.0 volts.
Assume the one cable feeding through the OBC is 3' long.
Assume the total cable length, including the 3' cable through the OBC, battery jumpers and others is 15'.
The voltage loss in 3' 2ga cable would be approx. 0.0468 volt
The voltage loss in 3' 4ga cable would be approx. 0.0591 volt
The voltage loss through 15' of 2ga would be approx. 0.234 volt
The voltage loss through 12' of 2ga + 3' of 4ga would be approx. 0.281 volt
The total voltage to the motor with all 2ga would be approx. 49.77 volts
The total voltage to the motor with 12' of 2ga and 3' of 4ga would be approx. would be approx. 49.72 volts.
The delta of 0.05 volts would be NEGLIGABLE.
Please keep us posted on how it goes. We love to see pics of these type upgrades!