I went through all that years ago on my blog. You're confusing the metaphysical distinction between nature and supernature, with the emergent distinction between nature-as-the-wilderness and anti-natural artificiality. So we can say intelligently designed worlds (cultures, cities, civilizations, etc) are virtually "supernatural" in that they tend to displace the mindlessly evolved wilderness, or those worlds supplement natural laws with higher order social and moral ideals.

So no, there's no self-contradiction here.