I agree that one of the costs for doing everything at the highest possible layer is the potential for mistakes. I don't think every application should
invent their own cryptosystem; I think most applications would be well-served with Nacl, and I think things like GPGMail show another good path forward.
I agree that it would be good if the lowest common denominator provided integrity checking, but as we can see with XTS, sector-level encryption makes that hard. Hence the article. :)