Many people today just want to say that metaphysics and theology deal with "the supernatural." For Aristotle, they deal with the natural world itself -- that part of nature that cannot be reduced to "telescopes and microscopes."
Even so, the deepest questions remain - the theological questions. As you say, the questions Leibniz asked "Why is there something, and not nothing? And why are things the way they are, and not some other way?"
God has revealed Himself in Jesus Christ, in the indwelling Spirit, in Scripture and in Nature. Even primitives will be held to account if they fail to notice His revelation in nature (Romans 1:20).
That is not a testable hypothesis. ;o)