Just got quotes back from Ocean Breeze and Flagship. Flagship wins on price. For two 24kBTU chillers, three evaporators (9k, 12k, and 18k), plus all of the pumps, tanks, controllers, etc, it's ~$13.5k, or roughly double the price for three self-contained units equal in rating to the chilled system evaporators.

For that extra coin, you get the redundancy Pascal mentioned, quieter operation, compatibility with a Webasto boiler, and lessened risk of long runs of raw water hose developing a leak and potentially sinking the boat.