To the first order the efficiency of the alternator (at a given power level and RPM and if matched to the load) doesn't depend on the voltage it's wound at:  Wind it with N turns of cross-section A and run it at 12 volts or 2*N turns of cross-section A/2 and run it at 24V and it gets the same current density and the same resistive losses.

(It's not QUITE dead-on:  You also get eddy-current losses and you'll get a TINY bit more with thicker wire.  But you can make it exactly the same by winding the half-as-many-twice-as-thick windings as two-in-hand of the thinner wire.)

On the other hand, when pushing a given amount of current down the feed wiring, cutting the voltage in half doubles the current.  Your resistive losses are the SQUARE of the current times the resistance, so doubling the current quadruples the losses with a given wire size - or requires you to use wire four times as thick to get the same amount of loss.  Copper is REALLY expensive (and insulation is cheap).  So if you're running high power you'd like to run high voltage to save on copper.

Same applies to the wiring within the "battery shack":  Bus bars, battery wire, switches, wires to the alternator, resistive losses in the batteries, fuses/fusible links, etc.  Also:  Currents over about 100A requires more expensive equipment and for fire safety requires wire thick enough that it's like wrestling anacondas.  So rule of thumb is to keep your load wiring down to 100ish amps - which means no more than about 1KW on a 12V system, 2 KW on a 24V, and use 48V for up to 4 KW.