here is the problem i see the chance of both batteries being equally discharged and charges by two separate alts is slim to none...first off the alts would have to able keep the batteries at exactly the same volts or it will fofce the 24 volt alt to over charge or under charge the second battery..for instance if the 12 volt alt charged the first battery faster than the 24 volt alt charged the pair the first battery would have more volts than the second possible fooling the 24 volt alt into thinking they are charged.this could cause the second battery to be charged at a lesser rate than the first battery and in time make the second battery fail.
Unless you have REALLY discharged your batteries, the alternator will be at full voltage almost immediately. If you regularly deep discharge your batteries, you run the risk of damaging your alternator and thermal runaway of the batteries, and GUARANTEE short battery life. Even designed-for-deep discharge batteries have their lives cut short with deep discharge.
The extent of your "charging" system is to apply a constant voltage. It doesn't observe the voltage/ current and change it's operation. It JUST works to maintain a constant voltage. If one alternator is malfuctioning, things will go awry; though this possibility exists with any system.
You are correct. If the "12V" alternator is at 16V and the "28V" alternator is at 26V, the upper battery will not be fully charged. If the "12V" alternator is low and 12V accessories are used, you may run the lower battery low and damage it. None of this invalidates the concept, though.
Also doing this doesn't give you the ability to run a dual purpose battery on the 12 volt side for camping and still be able to start the truck at the end of the weekend and charge both systems...
I was not disputing the value of this type of setup. That's really not the crux of the argument. However, don't think that your SLI batteries will last very long with this type of use.
I am a relative newby in the realm of lead acid batteries but the aformentioned arguments are first year engineering basics. Newby is probably a relative term. I have 10.5k lbs of lead acid batteries in my laboratory. If I didn't have a project deadline looming in Feb, I'd tackle this immediately just to prove a point. However, we should be able to argue the technical merits of ideas.