Thank you for sharing your thoughts and experiences, as well. A dual-alternator setup sounds quite complicated. Did you remove the air conditioner to fit the second alternator in there? I don't have a plow that big, just an 8ft Fisher Speedcaster I retrofitted to mount on my '97.
I think your point about the automatic cutoff is a good one, as well. I hadn't thought of it, but the voltage drop of running the hydraulics will (as you pointed out) probably cause the isolator to remove one of the batteries when I need it the most. Something more like what you have suggested is better. Does the battery isolator you use have relays or solenoids or did you have to wire the fat-gauge ground wires for the batteries directly into the interior? I'm thinking of exploring something like this but I know they also make electronic ones that will connect both batteries only when the vehicle is running. That might be something more like what I need.
My plow truck never leaves my driveway so I get away with some things that I wouldn't do in street driven vehicles. I am running large gauge negative cables directly from the battery terminal to the switch in the cab and back out to the engine bay to get grounded properly. There are better (more expensive) way of accomplishing the same thing.
And the second alternator mount was just a creation using some scrap steel and a welder. Cheap and works great but ugly.