The implication seems pretty obvious to me: according to the episode, as well as mainstream creationism, the human species is a desired end product of a project. This is the exact opposite of a natural process of evolution, where the human species is neither an end product nor a desired goal, but merely something that happens to meet the requirements of the day and survive until better things come along.
And "better" may well mean rats or mollusks or bacteria or other innovative solutions, whereas in the creationist or "The Chase" context a very narrow set of parameters is paramount and Man is superior to everything else.
In the episode, creationism triumphs over evolution - a perfectly plausible situation in a universe where humanoid intellect precedes us, as its desire to perpetuate itself is something we very well understand. IMHO, it's a gentle message: "Yes, that thing there is possible, too. In the special circumstances of fiction. And perhaps life is indeed fiction, rather than the more interesting thing we currently mistake it for?"