I'm not sure if there really is an issue with lack of oxygen and the flood. I believe that if you cover the globe with water covering the highest mountains, then the atmosphere gets displaced upward. So you will still be at sea level floating in the ark - the sea would just have risen and the atmosphere would have risen with it. The atmosphere would get a bit thinner though, because having been displaced upward on the global sphere means that the same amount of gas is now spread over a greater circumference. But the difference would not be so great as to make breathing very difficult or impossible.
There are lots of things wrong with the flood story and which disprove it. But I don't buy the argument about the elevated altitude making it impossible breathe.