"HOWEVER, it does not have separate charging outputs for two separate battery banks.."
It's best to inquire from each manufacturer what "separate outputs" means.
"separate outputs" is not an obvious issue. Modern electronic smart chargers DO have separate outputs but that needs explanation. On STATPOWER 40AMP 12 vdc smart chargers for example, from Xantrex, there are three separate outputs, designed for one per battery bank. All that means is when the charger is OFF the three terminals are not connected....so one low bank will not bring down the other two. The terminals provide common charge when the charger is on and isolation when its off.
BUT, it is ONLY the #1 terminal, on the left, (and described in the operations manual), that determines charge rate....so it's best to put your house bank on the #1 terminal, because that bank will normally be used dockside and will be lower than, say, the start banks....The higher internal resistance of fully charged start banks will limit their charge current so the arrangement works well in practice...
Aboard my Hatt 48 YF, I have three separate battry banks with two sharing different house load duties. I have three Statpower chargers, and the #1 terminal of each connects to a different battery bank....so I know all are always fully charged...and I have considerable backup redundancy....