I'm a little confused to your layout as to what is gravity versus what is pump fed, and it is definitely an ambitious but interesting plan!
I think you are right that trying to run a refugium, mangrove system and a algae turf scrubber will not work, as they will each make the other ineffective.
I like the idea of housing a "hatcheries" in a confined area close to but separate from the tank. My concern with things like that in so confined an area is always dissipating the inevitable heat build up our area is known for.