If your wire is long or small enough that there is a significant voltage drop across it, that means in your 2nd configuration each battery will see a significantly different load.
The battery farthest from the load sees the long wires as a resistance in series with the load. Thus, less current will be drawn from this battery.
The battery closest to the load sees very little resistance from the wires in series with the load. Thus, more current will be drawn from this battery.
Thus, the battery closest to the load will discharge faster than the others. This is probably not good, as it puts more wear on that one battery.
There is also a similar problem with dissimilar resistance between the batteries from the perspective of the charge controller. When the batteries are not full, the battery closest to the charge controller will take more of the current. Only if you are charging at a low enough current to make the voltage drop across the wire significant will all three batteries reach an equal charge.
Perhaps if the loads are also distributed across the wire, then there could be some merit to this system. However in that case, I think it might make more sense to run each load from an independent battery.
I would say the best solution is to use a thicker wire, which will reduce the resistance of that wire, and consequently the voltage drop and energy loss (and fire hazard, assuming a properly selected circuit breaker).
Another solution is to step-up the voltage on one end, then step-down the voltage at the other end. Or just design the entire system to work at a higher voltage. Holding power constant, increasing the voltage decreases current, and consequently resistive losses in the wiring. This is precisely the technique used by electric utilities, where wires are even longer.