hooking two batteries in parallel is very dangeous. There would be nothing to limit the current from one to the other, and a charged battery could easily source a hundred amps into a dead one. When electronics fail they often fail as a short circuit - so your current limiting circuit could become an inferno.
you are really better off using one charger per battery, because the charger senses the voltage across its terminals, and will limit itself to the battery with the higher charge
besides, if you have two or three 6 amp charges, and one fails, you are not dead in the water - if your custom muliti bat charger fails, or if FIRST says 'Hey you cant us that' you will be in deep weeds.
in fact, the more I think of it, Im pretty sure FIRST would not allow any custom battery chargers in the pit area - if it fails the battery could explode - imagine the resulting lawsuit when 20 or 30 people are sprayed with hot sulfuric acid and molten lead!
BTW - I assume you are not talking about charging the little backup battery this way too - you put 6 amps into that and you wont get out one chorus of 'pop goes the weasle' before it blows.