The only thing I can think of that caused the above issue is, because the earth went back to the engine bay, that whole run of cable let power through when the battery shorted out on the tub. Obviously, had it happened in the engine bay, there are very short runs of cable, so if somehow the battery hit the bonnet and blew all the fuses between it and the cars wiring, but continued to short out then there is only a short run of negative cable to burn out... with the above scenario, there is the same length of negative cable as positive, so if only the positive terminal of the battery contacted the tub and blew the fuses or breakers, then the power returning to complete the short circuit would travel all the way back to the only earth point, being the front of the vehicle.
Does that make sense?
Maybe it is worth putting a breaker or fuse of the same rating as the positive side on the negative side of an auxiliary battery mounted in the tub, if running the earth all the way back to the main battery?