My manuals are on the boat so I will provide some thoughts from memory. Perhaps my comments will provoke someone else, with more experience in these issues, to contradict me.
First, I own SM #331 which was originally equipped with Delco "sealed" lead acid batteries and a pair of Sentry battery chargers. I have tracked the wiring on the battery chargers and the alternator. There is no "master regulator" on our system. The battery chargers are wired directly to the batteries, as is the alternator. The only adjustable setting is that the Sentry chargers may be set to either "gel" or "free cell". The gel setting is a half a volt higher than the lead acid setting. Two years ago I replaced the original batteries with lead acid Trojan (non-sealed) batteries. I use the gel setting while cruising, because it charges the batteries faster and then switch back to the free cell setting when we are hooked up to city power at a marina. The 24 V alternator has a built in regulator and there is no "gel" or "free cell" setting on this. To boost the charging voltage, you would typically add an in-line diode to the field sensing wire between the battery bank and the alternator. This would drop the sensing voltage from the battery bank by half a volt and thereby boost the charging voltage by a similar amount. We have never done this and our voltages are almost identical to those you describe. That is, we do not have a 28.4 Volt deficit charging option, nor a 31 Volt desulphating option.
When under passage, I check out the number of ampere hours used, twice daily. Both battery chargers will provide a little over 60 amps positive flow, when combined. If the deficit ampere hours (from the Link monitor) is say, - 80 Ah, I would set a timer and run the generator for 90 minutes. After 90 minutes of charging, if the charge rate has dropped below 20 Amperes, I shut the generator down. If I need to run the water-maker or washing machine, I will then run the smaller (30 Ampere capacity) battery charger, at the same time, to "top-up" the batteries. Otherwise, we do not even try to reach 3 to 5 amperes trickle charging from the generator.
Hope this helps,