In Kingdom Hearts 1 and 2 Sora must become a mermaid to breathe in Atlantica. In Chain of memories he walks into the Atlantica door like it's nothing. If he still needs to be a mermaid to breathe underwater then there's no way he has an ability to breathe under it in Chain of memories (in between 1 and 2). If C.O's doors do indeed drive off of Sora's memories for each card then Atlantica would go by the same rules as before.
In conclusion, gathering all of this, the only logical explanation seems to be that Atlantica's water is fake in some way.
In Kingdom Hearts 1 and 2 Sora must become a mermaid to breathe in Atlantica. In Chain of memories he walks into the Atlantica door like it's nothing. If he still needs to be a mermaid to breathe underwater then there's no way he has an ability to breathe under it in Chain of memories (in between 1 and 2). If C.O's doors do indeed drive off of Sora's memories for each card then Atlantica would go by the same rules as before.
In conclusion, gathering all of this, the only logical explanation seems to be that Atlantica's water is fake in some way.