While voltage drop on both sides of the trailer follow the same rules, there is an advantage of using short & larger wire for the controller to battery side. As Brian noted, Wattage (power) loss is dependent on the wire size & current (W=I squared times R). The reason for using larger wire on the controller/battery side is the controller can only approximate battery voltage. Surface charge, etc produce inaccuracies. Instead, it determines its output based on the algorithms built into it, then goes into the various charging stages, often determined by time rather than voltage.
Low resistance loss is important because the differences between the various stages of charging (bulk, absorption, and float) are, in some cases, just a few tenths of a volt. For example, If the loss between the controller & battery is more than a few tenths of a volt, the battery may "see" Float voltages rather than the Absorption voltage the controller is producing. This results in much longer charging times, and may result in the battery never reaching full charge.
On the input side, you may lose the same amount of voltage due to resistance, but since the panel is usually capable of producing higher voltages than the controller output needs, the loss is not as important. In the case of a PWM controller, it just increases the on time to make up for the lost input voltage, resulting in the same voltage going to the output & battery.