The possibilities are that the sea rose to cover the mountains, or the mountains were once under the sea and have since risen out of the sea, or a combination of the two. The rate of rise now measured is just the remnant of the processes that occurred much faster in the past. Mountain building occurred as a part of the geologic processes that deepened the oceans to take the waters off the land towards the end of the Flood. Some mountains could have existed before the Flood, but none like the current Himalayas, Alps, or Andes in height. So, if the waters were not 9 kilometres deep, but much less, the question is no longer an issue.
Air pressure is caused by the weight of air above the point where the pressure is being experienced.
If the water was 9 kilometres deep, then the air that was in that 9 kilometres deep volume of what was atmosphere would have been pushed out and would then have sat above the water at 9 kilometers above the earth's former surface. However, if we assume the worst case scenario of the radius of the earth increasing by 9 kilometres due to the water, the surface area of the earth plus water would have been greater than the earth so that the weight of air would have been spread over a bigger area so that the pressure would have been less. But I fear, lest by any means, as the serpent beguiled Eve through his subtilty, so your minds should be corrupted from the simplicity that is in Christ. Answers in Genesis Ministries International. A member of the Gospel Communications Network .