Yes, I ran into this same issue (smart charger for 32v) a while back. My solution was to utilize the Outback 3232 inverter/charger to charge the 32v batt banks.
The charger incorporated into the unit is extremely smart and can be custom talored for any voltage for the various charging levels - bulk/absorb/float/eq in .1v increments. Works marvelously and will completely charge both batt banks from 50% to full charge in a fraction of the time of the oem charger.
The down side is that it does not have separate outputs for each bank so the banks must be combined into one big bank. Actually, I have found that this works just fine and all related info (Calder, etc) on this states that one larger bank is considerably more efficient/batts last longer than two smaller banks that total the same size.
However, by combining it would be possible to drain the combined bank to the point where the starter(s) would have insufficient voltage. We spend a lot of time in our cruising on the hook and have never had the slightest difficulty but it is possible.
Our replacement NL genny uses 12v to start so we have a separate source to charge the batts in the unlikely event that we drain the mains so much that they won't start the engines. If our genny also used the mains to start, as per oem, I would probably be less inclined to combined the main batt banks though it depends a lot on where you cruise.
Frankly, in the Chesapeake, I wouldn't worry about it much. In more remote areas or offshore, I would want the banks separate for piece of mind if the genny started using the main batt banks.