Correct. But we don't just go on structural similarities, as you already know if you've read the article.
The truly interesting thing is that the theory of evolution predicted that we would find very specific fossil sequences, and we found them. For example sequences from land dwelling walking mammal to modern cetaceans. You are right, we can't prove that those intermediate fossils are ancestors of modern whales, but wasn't Darwin the luckiest man alive to predict that such fossils would exist, long before they were found, unless his theory is correct. And that is just one example amongst many thousands of confirming data.
Pretty much every way that we *could* have discovered fossils would have disproved evolution. But what we actually keep finding, and the discoveries keep appearing, are finds that are consistent with the theory. They are consistent with respect to the geological strata that we find them in. They are consistent with respect to radiometric dating techniques applied to the rock we find them in. They are consistent with respect to the geographical regions we find them in (what creationist would have specifically predicted finding marsupial fossils in Antarctica, as evolutionary scientists did *before* they were found).
It isn't just fossils either. The theory makes preidictions about what we'll find when in the modern world. eg remote oceanic islands all have unique species of flightless birds, no two islands share the same species, easily understood using evolution, incomprehensible using a design hypothesis. Every one of the many millions of species currently extant fits into a nested hierarchy of form and function, and as we go backwards through the geological record the hierarchy shrinks (with a tendency towards simpler and simpler forms) just as the theory of evolution predicts. As I say if evolution is wrong those evolutionary scientists are the luckiest people alive to just keep making all those successful predictions of field data.
"You are right, we can't prove that those intermediate fossils are ancestors of modern whales, but wasn't Darwin the luckiest man alive to predict that such fossils would exist, long before they were found, unless his theory is correct."
Read some of Darwins later writings in which he himself calls into question many of his conclusions. Predictions don't prove anything when you already know the outcome of the prediction when it's made. You might find structural similarities between one skull and another, but the difference between them are huge when one is trying to claim this animal evolved into that one when there are no fossils found in a series to demonstrate how those differences changed over time. I'm not saying evolution is wrong, just misused in explaining the differences between species. Minor changes in species over time could happen. But one species completely evolving into a different one? There is no evidence which supports this contention.
"They are consistent with respect to the geological strata that we find them in. They are consistent with respect to radiometric dating techniques applied to the rock we find them in. They are consistent with respect to the geographical regions we find them in . . ."
I'm not following how these "consistencies" support evolution of one animal into another. I see this as evidence that intelligent design knows what belongs where and with what else. And Darwin predicting that fossils would be found doesn't prove anything except that he was observant.