I actually ended up speaking with two NOCO techs in regards to multiple bank on board chargers. They both told me they have safety features inside the system which would never allow for one battery to charge or drain into the other battery.As for power "back" feeding through the charger, shouldn't happen depending on how it's wired.
Battery chargers use a rectifier to change ac to dc.
When the charger is not "turned on" I don't see how it could affect the two batteries.
If it did have a short the charger should not work or might be in a rather dangerous condition.