*twitches at the mention of "genetic memory"*
I do like that word "enculturate", though, that's a keeper

.
I don't think you have to reach for an actual literal basis for these myths and such - the extrapolation from small things to big things seems pretty common in folklore. For example, small floods are pretty good at killing people, regardless of swimming ability. Water as a massive cleanser and messenger of death has a rather perverse poetry to it when applied to desert nomads, too

. Also, like others have said, a flood as a tool of cosmic genocide is not universal.
For another example where I just invent things, we could look at the giant lizard folklore, dragons, etc. Should we extrapolate from this the idea that there were once massive lizards throughout the world such that the stories were passed down, but they just couldn't fly? Should we postulate that people found dinosaur fossils? Or are men's imaginations wild enough as it is without needing a significant basis in reality?