I would assume that if the O-ring is intended for a fuel tank cover, that it is fuel-resistant. Use something like Rector Seal (gas compatible thread sealant) if you're worried about it.
Most electrical systems use the negative side as a common, and switch the positive side. No particular reason on boats, as far as I know, just common practice. As you said, there is no "ground" per se, as there is on cars (where the cathode is tied to the chassis), so you could, in essence, switch anywhere along the circuit.
That may, however, cause problems later when someone else tries to assist you with electrical problem resolution. Better to stick with convention, IMO.