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?

Item 1 - Your batteries wouldn't be very useful as the diode would allow current to flow from the alternator to the battery, but no flow out of the battery. Both would be charged at the same rate though. There would be no way to completely isolate them from each other if they are going to feed the same electrical circuit. Now if one was just a starting battery and the other handled the rest of the electrics, then yes.

Item 2 = the coil winding would most likely burn out before the coil exploded. In a points system the coil is only energized if the key is on AND the points are closed, not 100% sure about electronic ones though. Coil saturation is something different, it is, essentially, when the coil's magnetic field is completely built up and can grow no more.

Yes. that's the idea. EFI wiring can be problematic if not done with dedicated +/- so my thought is two separate circuits. I wouldn't even ground the EFI system to the body, I'd use +/- buss bars. Only the starting and accessory circuits would be grounded to the body.

That seems unnecessarily complex. I can't think of any factory EFI setup like that and I sure am not doing that with the microsquirt EFI setup for my 51 Plymouth, If you are worried about some noise on the line messing up your computer, you can add filters to deal with that on the main feed to the computer as well as making sure you have good, clean grounds done in accordance with your EFI supplier's directions.

If you are you using a "isolater" power from the alternator will be divided between the two batteries. The regulator is only looking at voltage output to them both(before the isolator).
https://wagan.com/blogs/news/dc-to-dc-battery-charger-vs-battery-isolator

You can't isolate both battery from the alternator if it has to charge them both. The issue is what does the VR see voltage wise. The fully charger battery would present a high voltage to indicate lower field current. But the charged battery would discharge to charge the low battery until both were at equal voltage. If one battery different from age/use, you would have an imbalance.

Charging multiple batteries requires a smart system. Paralleled batteries and alternators/generators would require a governor system. Otherwise load sharing is not equal.

They would be isolated from each other by diodes - which are basically a one-way gate. But I understand what you're saying about the "full" battery telling the alternator not to charge.

You have to explain your diode circuit to isolate them since it sounds like you want them to operate in parallel. Can't have your cake and eat it too. Plus what is the rating of these diodes? 50, 100, 200, 500 AMPS? There is a reason batteries run in parallel, or they are isolated with switch and used as a backup.

Read the entire thread.

One is a start only battery, the other will handle the rest of the battery chores, such as they might be

In that case, yes you can use a diode to isolate the charge feed to the start only battery,

Not trying to be a PITA but I'm pretty sure all the diesels I've had, both GM and Dodge simply paralleled the two batteries. I could be wrong though.

They probably do ... but they're both powering the same stuff.

I'm thinking one possibility is this:

Use an alternator that does not have an internal regulator
use an external regulator for each battery
isolate each battery with a diode in the charge line from the alternator