First, multi-bank chargers which are programmable so that the charge profile for each bank can be seperately specified to suit different battery technologies, are readily available: Victron & MasterVolt have produced these for some years and most recently, Charles Industries has released a new "Intelligent Marine Charger" (IMC) series that does this. These were favourably reviewed in PassageMaker last month. It is really no big deal and since different battery technologies SHOULD be used for different on-board applications, they are a good idea. Second, it has been pointed out on another post that an alternative approach is to have a single charger focussed on the House bank and to charge start/genset/thruster/electronics batteries using programmable (for different battery technologies) charge-transfer devices off the House bank: products like Balmar's Digital Duo Charger or the Ample equivalent. Third, most competent installers of battery chargers will use the dip-switch or other control devices within the charger to de-rate the maximum output of the charger at least somewhat: for a 120A charger, it is not uncommon for an installer to de-rate these to 105-110A, for example....just so the charger is not operating right at its design limit. Further, the max rated output of a charger is achieved only at a specific ambient temperature, most often 20C; if you are in Florida in Summer...or if your charger is in a hot/poorly ventilated space, it will de-rate itself. (Good idea to install a brushless computer fan to cool the charger - or inverter - adjacent to help minimize this ambient temperature de-rating). Finally, if you only have a 440AH bank, that is not very big by today's standards and the C20 rule would suggest that for AGM or Flooded, the max charge should be only 88A anyway. C25, the absolute top end, would require 110A...not 120A...and I cannot imagine why you would go there. If your biggest concern is minimizing generator run time, then go for AGM's as they will accept the 88A charge for longer (ie they will stay in Bulk Charge mode longer) and so will re-charge faster overall....but you are reducing generator time at the expense of higher-cost, more charge-volt-sensitive battery technology. If you really want to impact genset run-time, get a quality, multi-stage external regulator that has BOTH battery and alternator temperature sensors so your alternator(s) are operated at maximum output consistent with not overheating either alternator or battery; and then to take it even further get a high-out alternator (120A+); and if you have twins, direct the charge from both alternators to the house bank. You will then find that even short cruises of 1-2 hours between anchorages put a lot back into the House bank such that genset operation for battery charging can be just something that happens in the background when you operate the genset for cooking, water heating, air-con or whatever.
