It is a fact that these fossils have a mixture of modern whale features and features from terrestrial mammals. That’s what makes them transitional, and no stories are needed.
That’s not what happens. They use as many genes as possible, and the contradictions are right where we would expect to see them if evolution is true. When you are dealing with deep nodes with little genetic data you would expect contradictory trees for different genes. However, the contradictions are still well within the expected phylogenies. It isn’t as if some mouse genes have them more closely related to squid than to squirrels.