You forget the custom among ancient and primitive peoples of regarding themselves as all of humanity (witness many linguistic usages--for a recent one Allemani, form which the French name for Germany is derived).
The Holy Scriptures were not composed by and for modern rationalists.
I agree, but in the case of Noah's flood, the theology of the story does not make much sense to me if the flood did not wipe out most of humanity.
Perhaps I'm missing the broader point.
What's your take on the story? How, for instance, do you interpret the post-flood covenant?