I neglected to point this out, in the article, but the accompanying sample solution includes a "post-build" makefile project, which kicks off NDoc after every Release-mode build.
Check out the files in the "xdeploy" subfolder, to see how the magic is done. This technique is extremely useful for many, many tasks -- not just NDoc!
(Mind you, I love NAnt, but I'm not always able to impose its use across your every development team I come across. NMake is everywhere, and rigging it up to run before/after your primary project is a valuable technique, until some future version of VS.NET provides explicit support for this.)