The reason is, wet cells and AGM batteries require different charging profiles, or regiments. Overly simplified, wet cells, like a cranking battery, get charged a a varying voltage, anywhere from 13.3 volts to 14.4 volts, but the amps going into the battery stays the same (since too many amps will cause the battery to boil over). AGM batteries require a constant voltage, 14.2-14.6 volt for most of them, but the amps into can vary wildly (because of their low internal resistance they can handle far more amps than a wet cell can).
So, basically, wet cell is constant amps with varying voltage, and AGM is constant voltage with varying amps.
One charger cannot do that, so whatever the charger is hooked up to, all of the banks need to be the same battery type.
Balmar, another boat-centric manufacturer, has external voltage regulators (Xantrex does, too) made to go with their Balrmar alternators, where you can use a single alternator and an external regulator (the DuoCharge) that outputs two different voltages to charge banks of different battery types. The way they works is, you hook the boat's (or vehicle's) alternator directly to the battery bank instead of the vehicle system, which then charges the battery bank directly with the required voltage, and then from the bank you run the DuoCharge to the vehicle's system and it'll output the required voltage for the system. One alternator, dual regulated voltages, two battery systems charged.
The major drawback is that the DuoCharge only outputs 30 amps max to the vehicle's system, which is fine for a boat with a running engine, but not so much for a Sprinter, truck or any vehicle that needs 50 to 80 amps just to run down the road.
So you need some other way to output the correct voltage to each of the different battery types, yet still have enough amps go through. Ideally, multiple alternators would work. Some Sprinters (the passenger models with rear AC) already have the bolt holes in place for a second alternator right there on the engine. But the cargo versions don't, and thus require some modifications.
A company called Averc makes a dual external regulator that's used a lot in Sprinters in Europe, but I can't find one here, and it's expensive.
Bottom line generally speaking is, if you want an AGM battery bank, then you need an AGM cranking battery, so that everything all around is the same.
But back to the CRS1 (and CRS2 two bank, and CRS3 three bank), it's just like your charger, pretty much, except the input voltage and current comes from the alternator instead of shore power. The have another version of "Charge On The Run" chargers that is both 12-volt and 110-volt (I think it's called the Xtreme or something like that), but they are getting rid of those (if they haven't already) in favor of the CRSx models and a separate shore power charger like yours, rather than have a dual unit.
Basically what it does is, it works like a separator/combiner/isolator and will charge your trolling battery while you're under engine power moving to another part of the lake. Except that it's more than just a separator/combiner/isolator in that it's a real charger that will shut off when the battery bank is fully charged, or will do a trickle maintenance charge, as needed. Right now, with a battery separator, which is just a solenoid relay/isolator, when I'm running down the road and the batteries are fully charged, the alternator keeps pushing volts to the bank anyway. Sometimes, especially in very hot weather, that will result in boiling over and overcharged batteries.
The CRS1 works like a separator/isolator/combiner in that it will only push charging current to the house bank when then engine is running and the cranking battery is being charged. If the charging current to the cranking battery every drops below 13 volts it shuts off. Same as the separator does.
I can keep the separator I have, which is in between the cranking battery and the battery bank, and it closes when the engine is running and send the charging current to the bank, but I can install the CRS1 in the bunk. When the separator engages and sends power to the house bank, the CRS1 will engage and charge the house bank just the same as if I had it plugged into shore power charger, with all of the smart charging stuff that goes along with it.
OK, I've just convinced myself, and it's something I should have done a long time ago.