You shouldn't need to worry about the libs folder. You will want to merge the "boost" subdirectory of this with the location of your boost headers so that it matches up with numeric, etc. and the includes of where the headers are in the sample code. After that, you should be in business and don't need to do any building of the libs directory. Or at least that is what I did for the LAPACK setup using Intel MKL.
Also, a newer version of the boost bindings is in progress which is looking great. I am not sure of the exact plans for atlas, but there seems to be BLAS binding support in progress and may actually work. So depending on the time horizon of your project, you may want to consider testing out some of the newer BLAS bindings (if this is bad advice, I apologize to the developers of the bindings).
As for noalias... I don't know the answer of why it wouldn't help, or how much it possibly could help. Just to verify though... you are setting NDEBUG as a preprocessor instruction? That could make an enormous difference.