I've looked at a wiring schematic of one before and got a headache. Don't know what the point of it all was? My Dad had a 4010 Diesel when I was a teenager. He had our family mechanic who is a pretty sharp guy come over to do something to it and he was pretty dumfounded by it. He was a mechanic in the Air Force with 20 years experience after that by the time I'm thinking he was over so it certainly wasn't his first rodeo with 24 volt systems either.
Yes, with one battery having its negative post grounded and the other battery having its positive post grounded, it can be very confusing. But if you just consider that the chassis of the tractor is being used as a battery cable, it might help to clear things up. One thing to avoid is having any power consumer grounded at all. Very difficult when the vast majority of radios etc. are built negative ground. So, the best solution is what JD did when they put the alternator on the diesels and make it negative ground like 99% of the vehicular electrical systems are.
As to why JD designed an electrical system like that, the only explanation I can think of is to cause the owner to return to JD for service.