due to the boundary layer being much bigger, which is what you always say is what makes the ATS work, right?
No, smaller is better.

You have to see the "bucket waterfall" design here
Yes, there is a reason I posted this simple one first.

what about using a venturi system on a powerhead to deliver the air instead?
Taken care of

However I think salt creep prevention, especially if you plan to not change a lot of water, is really very crucial
Taken care of

The main problem I see in the new design is algae growing on the walls of the scrubber chamber/walls of the tank. Is this actually a problem?
A toothbrush should fix it.

one of these setups would be pretty awesome for raising baby fish
Yes fish do love to eat fresh green algae.