Which is why have less confidence on how, but more confidence that there is somehow a plausible natural explanation (though we cannot rule out God’s action either). We have too many possibilities for “how” it evolved, so the claims that “there isn’t just enough time” or “we can’t provide the specific mechanism in this case” now fall on unsympathetic ears. With so many complex and interacting mechanisms, we don’t expect to untangle them in many cases.
However, neutral theory gives us clear and quantitative tests of common descent. Our confidence in common descent, therefore, has only grown.