Yes I had meant to post a reply to your thread but ran out of time this morning and this one came up in my search. As far as I know, you can't charge the two completely different (different voltage, maybe different chemistry) battery banks with one charge controller. Well, one charge controller can do the three things you listed, one at a time. It would need to be rewired and reprogrammed to switch between them.
Using a 48V/12V converter would probably work most the time because if its voltage is at least 13V, it is acting like a trickle charger, keeping the 12V battery topped up and providing power to the 12V system. It there's a problem with the 48V battery or converter and the 12V battery gets drawn down, the 13V when it's available again may be too low to effectively recharge the 12V battery. But maybe the 12V battery's capacity was enough to get through the emergency and it could be charged off board or with a portable charger. Or, maybe you'd be away from port and have the time to rewire and repogram the MPPT to charge the 12V battery with the solar panels.