It is all about Ohm's Law. Efficiency of electrical flow will affect performance of systems.
The less resistance your system have the better it will perform b/c you are not wasting that finite electrical power to friction.
Quality conductors of sizable gauge will allow your charging system to work less to provide a stable power source to feed all the electrical needs of the vehicle. ie; Spark, Sensors, ECU, PCM, modules, et al.
While, Yes, The alternator becomes the primary electrical source after the engine has been started.. the battery is still within the system. If the alternator/generator have to fight to keep the battery charged to a set limit dictated by ECU then it will cause a strain and eventually make the vehicle's electrical system less stable. Overworking the alternator and voltage regulator.
basically, better cables will allow the alternator to charge your battery more efficiently with the voltage regulator not being overworked, thus providing a more stable electrical power to rest of the car. Lessen the chances of faults. Many computer modules and ECU work in the very sensitive 5-volt and milliamp range.