If you plan to have the system professionally installed then I think one hi capacity compressor and two separate plate systems with their own thermostats is probably the most cost effective way to go. If you are DIYing the install, then a couple of prepackaged systems are probably the best choice.
FWIW...I've had two AB units in the past and on the present boat, switched to the Seafrost DC5000 1/2 HP compressor for my large and separate 2 box freezer/fridge system with excellent results. It demands a large battery bank due to current drain, but onl remains on for short periods and freezes the plates in short order due to the current so the net use of electric is quite efficient and you don't have the fridge running 75% of the time in the tropics. Not a cheap system but worth considering given your configuration and large battery bank.
12 VOLT DC 5000