You bald faced liar you. The first part of your misquote from Madison was his lamenting the lack of a BoR in the Constitution. Which was later added. In fact, several States registered their opposition to the Constitution UNLESS the BoR was added as it was generally understood that the US FedCon would supercede their own State Constitutions.
You may be right about the second part. I found this quote on the Internet and it was implied that Madison wrote this in a letter to Jefferson after the adoption of the BoR. He may have written it before (after all you shouldn't believe everything you read on the net) and if that's the case then I'm sorry (no lie was intended).
As to the first part regarding the proposed amendment it is a quote from his own Introduction to the BoR in which he presented the new proposed amendments and among them a specific amendment which would apply certain restrictions to the states. For me it is clear that an additional amendment wouldn't be necessary if Madison believed that the BoR would directly apply to the states.