Behind the theory of classic evolution lies a metaphysical explanation for the universe: that life "progresses", from simple to complex, from the more fundamental to the more sublime, from problem to solution. The metaphysics of evolution is very much rooted in the philosophy of positivism and progressivism. It is anti-religious not in the sense that it is against the idea of a God, necessarily, but in the sense that the concept of a God is not needed to explain the natural world. God is irrelevant.
One does not hear debate on the metaphysics of evolution very often, and that is a shame. The philosophy of Progressivism, to me, seems more like wishful thinking, than a real explanation of why things are the they way they are. Is progress absolute? Certainly any objective evaluation of history, with its long record of extinctions, would seem to argue otherwise.
Regarding the Bible's metaphysics, however, there is absolutely nothing in common between progressivism and traditional Christian teaching. The very first chapter of the very first book lays it all on the line: God said, "Let there be light. And there was light..." and so on, for 65 more books. The doctrine of the Bible is that "in Him we live and move and have our being." This couldn't be more orthogonal to the doctrine of positivism.
So, while the Pope may rightly observe that a changing creation is still a creation, I'm not sure that really gets to the heart of the matter, which is a metaphysical argument about origins.