The NDAA did exactly what this bill purports to do: leave intact an unfortunate status quo. Almost nothing people say about it on message boards is true; it has become a shibboleth for "I pass along public policy gossip without verifying it".
But did it leave it intact or did it enforce it? Why did they need to write in NDAA too that they can do that if there already was written in another law?
I don't understand the first question. The answer to the second question is that the powers granted to the executive under the 2012 NDAA (there's an NDAA every year) are more limited than the blanket authorization to use force granted in 2001.