More speculatively, there was apparently a vapor canopy before the flood, but this alone would not have enough water to cover todays mountains. (But who knows how high the highest mountains were before the upheaval that caused the flood.)
The ark of Noah protected from God's wrath. (The ark of Moses is a type of protection from Satan's wrath; the ark of the Covenant from the condemnation of the Law.) The storm of God's wrath pressed on the ark, not on those inside, and on Christ, not on those in Christ. In Psalm 42:7 the Psalmist cries "All your waves and your billows are gone over me."