Have an idea but need some input ...

item 1)
Lets say you have a vehicle with two batteries and they are both charged by the same single alternator. HOWEVER, the batteries are isolated from each other by diodes in the charge wires from the alternator.
What happens if one battery has a full charge and the other does not ? The regulator in the alternator will want to charge the low battery. But what happens with the other battery - would it be damaged from the continuous charge?

item 2)
I've heard of "coil saturation" and I know that very often ignition is left "on" without cranking the engine. In these cases what stops the coil from literally exploding?