I recently installed a system following TT's description for the reasons he outlines. Part of that work package was upgrading the stock alternator to 170a externally regulated, so I can happily bulk charge at 130+ amps from the main motor. The DC-DC chargers are rated at 30 amps.
In talking to sailing friends and living with my new system for a month underway I now understand why that might be overkill for some. In my case I also added a solar array, and in fine weather my house bank remains charged by solar. And I can bulk charge from shore power or generator. In practice I don't really need that capability. If I look at the $$/utility for the alternator/regulator upgrade it doesn't score nearly as well as solar, for my case at least.
With older/smaller motors that don't have serpentine belts it's hard to install a high amperage alternator, so I get the strategy of living with an OEM setup and limiting charge current through a charger. Make sure the charger isn't rated for more than about half the your existing alternator rating though, or you may cook the alternator without heat regulation. You should also be able to set the charger to start only when the starting bank is charged to guard against peak loading on the OEM alternator, if that's a concern.