Sea of thesis,and air breathing objects

[Etaoin Shrdlu]

To your first point: The AotF "liquefies" the air around the holder. (imagines a "cloud" of water surrounding a suitable commander. Holds that thought, as it might affect things later.)
Can't help on the others, but since tritons no longer "fly" underwater, that makes them so ultra-sucky you wouldn't believe...
(little more thinking)
Although I could imagine that a spell like what you propose may have some reason, make it a ATL-OCE-RYH national ritual (like Soul Gate (ERM) or Carrion Woods (PAN) if I understand those new mechanics correctly, likely I don't) they could put in the globals screen, meaning only one could have it at a time! Say, high Ench, W6+, 100W to cast, valid until dispelled or death of caster? All we need now is a name for it.
Alternatively, as an item, to be a counterweight to the Pills/Manual of Water Breathing and Barrel of Air. Downside: the affected units would have to stay within range of the holding commander. (see above) Second downside: what happens when an enemy (non-amphib) unit gets within range (for something the effect of the Barrel that's a 25-square sector) and is now surrounded by a "walking" wall of water? You see the problem (and I just thought of it while I was typing this!) Implemented badly, this could be hideously overpowered.