Response: "It's an airplane; it can become a submarine but usually only once and doesn't take off again."
Obviously the solution is to re calibrate our notion that "sea level" is a uniform base of the atmosphere. Its baked in to so many systems as an assumption tho; it might be easier to fill in some valleys instead.
If we plane the earth nice and smooth all over, will we have gentler weather? Or just collect it all into large, static super storms?