The receding of the waters after the Flood could indeed explain this. If the waters had gone over a ridge, and the whales are doing OK in a deep enough pool, but then the waters recede and the ridge traps them in a now diminishing pool—yes, that would fit the case perfectly. I’m not saying that IS the explanation, but it is a realistic possibility. It could have been THE Flood, or perhaps another flood of sufficient size. An analogy would be when the tide comes in and then things are trapped in the tidal pools when the tide goes out.
How about this. Maybe that was a shoreline at one time and that’s where the whales beached themselves. It’s not like it never happened before.
No.
The article says ancient whales and it happened between 2 and 7 million yrs ago. You mention “the flood” which implies noah’s flood. Noah wasn’t around 2 million years ago.