The underlying fallacy is that the Bible has a single message. The Bible is a collection of works written (and sometimes rewritten) over a great deal of time and within varying cultural contexts, often reinterpreted to try to fit it to new beliefs. Modern Christianity itself is the product of development and change and exists in a cultural context quite different from that of the first Christians.
The Flood story in particular is old, predating even the origins of what is now Judaism. Even the version we have in Genesis is a merging or two stories derived from that original. Why should we expect it to have a message consistent with modern liberal Christian views ?
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