Suppose that God made physical stuff (say, particles) be arranged just like in a butterfly, but he did not give (either directly or by some general policy) a butterfly form. Then we would have something that looks just like a butterfly. And to the extent that butterfly behavior is ultimately predictable just from physics, that bunch of physical stuff would behave like a butterfly. There wouldn't be a butterfly there. In fact, there wouldn't be one thing there: just a bunch of physical stuff.
Now, we are not yet in a position to know how much of the physical behavior of organisms—especially non-human ones—is predicted by the physics. Let us suppose, however, that it turns out that all the physical behavior of non-human animals is predicted by the physics. (Humans have free will, and that's a different business.)
Now let me tell a story. I don't think the story is actually true, though it seems basically[note 1] logically possible:
God created a physical world and had some chemical stuff come together in a way that "reproduced". And then evolution took over, and bundles of physical stuff that were better at survival and reproduction reproduced more, until we had bundles of physical stuff shaped like algae, trilobites, trees, dinosaurs, birds, horses and apes. But there never were any algae, trilobites, trees, dinosaurs, birds, horses or apes. Finally, not too long ago on a cosmic scale, there came to be two bundles of physical stuff that were physically rather like humans. By this point, there was no physical stuff shaped like trilobites or dinosaurs, but there was physical stuff shaped like algae, trees, birds, horses and apes. And God then said: "Let there be algae, trees, birds, horses, apes and many other organisms", and he created forms which informed the algaelike, treelike, birdlike, horselike and apelike bundles of physical stuff, and all sorts of other bundles. Thereupon, there were birds, horses and apes, though things didn't look any different. Finally God said: "Let there be humans", and he created forms which informed the human-like bundles of physical stuff. And there were humans.
This story is fully compatible with naturalistic evolution. Indeed, the only bar to the possibility of this story would be a vitalism on which physical stuff does not behave like living organisms. On this story, there literally never have been any dinosaurs. But there will have been bundles of physical stuff arranged dinosaurwise, and that's all many a biologist thinks a dinosaur is anyway.
But since bunches of physical stuff can't be conscious—they need soul, i.e., form, for that—then on this story there was no consciousness before human beings came on the scene. This is theologically attractive in that it enables us to hold that suffering came into the world through human sin. For we can continue the logically possible story thus:
When God created the forms of all the organisms, he miraculously arranged things so that no organism would suffer, miraculously making a harmonious state. And he put humans in charge of this delicately balanced system. Humans, however, quickly came to freely reject God's sovereignty in the system that he put them in charge of, and he reluctantly removed his miraculous protection from the system in deference to the authority he granted humans. And so humans and other animals came to suffer.
This story is also interesting in that it is yet another way to reconcile naturalistic evolution with the not dogmatically required but still somewhat attractive theological idea that all the organisms there are were directly created by God. For the story makes clear in a Thomistic setting how naturalistic evolution only explains how we got to have the physical stuff shaped and behaving like algae, trees, birds, horses and apes. God's creation is needed to make this stuff into actual algae, trees, birds, horses and apes: forms need to be put in. (Compare how in Genesis we are told that God made Adam from the "dust of the earth", i.e., physical stuff.)
The main reason I don't like this story has to be with my being an eternalist. I think past (and future) objects are real. And I think reality will be more wonderful if it really contains trilobites and dinosaurs, not just physical stuff arranged trilobitewise or dinosaurwise. So while the above story is basically logically possible, I don't think it's actually true, because it seems likely that a God whose goodness spreads itself out creatively would be likely to create forms for physical stuff arranged trilobitewise and dinosaurwise.
But there might, nonetheless, be aspects of the story that we can adopt. In the story, creation was safeguarded by God's taking bundles of physical stuff and giving them form. We can posit this in a more commonsensical evolutionary story. Maybe the gametes of two dinosaur parents involve some mutation that makes the offspring be particularly birdlike. Then God can simply prevent the offspring from being informed by a dinosaur form and then instead make the offspring be informed by a bird form. This is still direct creation of birds from previously existing physical matter. And while higher animals prior to the first human sin were conscious, we can suppose that God in his love miraculously prevented any instance of conscious suffering that wouldn't be on balance good for the animals, say by miraculously preventing pain qualia or in some other way. But this divine miraculous intervention perhaps ended (though perhaps not!) when Adam and Eve rejected God's rule over the earth they were put in charge of.