Because they didn't.<quoted text>
There's a glitch in the story for pro and con. Both sides are 'assuming' that the earth at the time of the flood looked than geographically as it looks today topside and sea floor wise.
That the world just somehow flooded itself without any physical trauma as in volcanic action/earthquakes.
The writer actually describes something they should not have even been able to have guessed correctly that science has shown actually takes place on the sea floors today. "...all the fountains of the great deep broken up,.." The writer is actually describing water being pushed up by volcanic action through the crust of the earth through the sea/ocean/lake floors to add more water to what already exists topside.
The point shouldn't be whether an invisible being caused this to take place. The point to be wondered about is how the writer was able to describe volcanic activity that takes place miles to thousands of feet below ocean and sea water levels. A volcanic heated vent on the ocean floor large or small spills out vast quantities of heated water. Volcanic vents on land don't usually do this in the same manner as on the oceans floors that this writer would have been privy to have seen to have written about. So how did they make a best guess and guess it correctly?
Underwater vents are cooled by the huge mass of surrounding water, but volcanos on land throw out lava and magma. If you claim that there's so much water being spewed out at such tremendous forces and quantities as to flood the entire world the water would evaporate as steam. What's more if you're claiming the entire world's geographical landscape changed along with it, then you are essentially frying the entire Earth.
Noah's boat is only made of wood.
If humanity was to have sprung only from his family (SERIOUS genetic issues aside) then quite literally there is no-one left alive on planet Eatrh today to talk about it.
Now we can get back to the issue of your invisible magic being. None of this is a problem for invisible magic wizardry. For when faced with an absence of, or contradicting evidence, simply invoke the magic wizard who waves his wand and fixes everything how your favourite religious book says it is.
Evidence does not matter.