If you search other sites you will find posts about that system with gas motors. They use the second battery for an rv and charge through a battery isolator. The second battery doesn't contribute to starting the truck motor. On one of those other sites one guy said that his battery didn't last long so he installed a dual purpose marine rv battery. When you run an automotive battery down to 11.x volts it isn't going to last long at all. OP is on an rv site so I'm assuming he has an rv. If he hasn't been sitting camped out on the second battery he may never have had battery trouble. If he's unplugged from the tow vehicle and running on shore power or the rv battery he's never discharging second batt.
Without looking at a schematic or researching more I'm not sure what to say about not using a second battery. My guess is that if you removed the second battery, because of the isolator when you park you would not see power from a battery to the 7 way. If the truck was running it would seem that the isolator would pass power to the second battery circuit and on to the 7 way. The cables would obviously need to be covered properly so no arching and fire hazard occur.
This is just speculation so dont do anything on what I'm saying. If it was mine I'd probably install a dual purpose battery in spot 2. Someone else may show up who has this vehicle and done it. It all seems like a waste if it was actually used for the rv. Who at GM thought that an auto battery should be used in this manner? Maybe I'm missing something and someone will help out here.
I also seem to have read somewhere that some isolators wont pass power to battery two until it sees battery one fully charged.