I don't have any advanced degrees - I do have Rat4Spd on speed dial.
The REASON that I did not wire the 12 volt alternator to the existing 1st or 2nd battery in the 24 volt system is because I want them independent of each other. COMPLETELY.
This way, when I'm at DIRTBAG and I drain the 3rd battery (wired to the 12 volt alt) from running a microwave for burritos or a blender for margaritas, I still can start my truck. I won't need a jump, I won't need a push, I won't need anything, since I left the 24 volt side alone. And, as a side benifit, if a battery on my 24 volt side takes a dump, I can steal the 3rd battery to try and help things out.
Call me racist - but my 12 volt stuff doesn't mingle with my 24 volt stuff. 12 volts are for toys, 24 volts is to get me home.