I think the answer "that is the way they made em" is about as good as it gets from a technical aspect. Light bulbs and motors will not care if you change from neg to pos ground. What may care is a generator that is used to one way and if I recall correctly while your ignition will work it is hard on teh contacts when you change grounding.
Best bet LEAVE IT ALONE
MARK YOUR BATTERY POSTS WITH PAINT
MARK YOUR POS POST CABLE WITH RED TAPE
Dan Bentler