I don't really want to get into the 'does the NEC apply' argument.
I'd consider the following: You can use conductors in _separate_ non-metallic cables as part of the same circuit. So for example you could run two 12-2 UF cables side by side to have 4 circuit conductors in addition to EGCs, rather than cheating and using the bare wires as circuit conductors.
Since you control the alternator (rewound) and also control the load topology, you can split the load up across multiple cables without actually putting conductors in parallel (connecting them at both ends to form a single conductor).
For example: you could use three 12-2 UF cables to supply 'hexaphase' power from alternator to rectifier. This shares the load across 3 cables, but since the supply end is from separate alternator coils, and the load end are separate rectifier connections, the conductors are not in parallel. OCPD would be strange; I've never seen a 6 pole common trip breaker assembly, but perhaps the maximum short circuit current of the alternator is such that OCPD is not needed? (not sure if there is a way to get around OCPD requirement if the source cannot supply more current than the ampacity of the conductors...)
Or you could take each of the alternator coils and use it to supply a _separate_ single phase rectifier, giving you 3 separate DC outputs. Run these 3 DC circuits in separate cables, combine at the load end.
You might consider voltage doubling rectifier circuits, as another approach to getting a more efficient system voltage.
-Jon