Agree with what your saying, there are some gems in html5 boilerplate but when it comes to them defining what structure you should use for assets etc or libraries you should I simply disregard them and pick and choose useful pieces from them.

Those kind of boiler plates tend to cover all bases which is great but its up to you as a developer to decide what suite the project.

Some of the best parts of html5 boiler plate for me is paul irish’s conditional html tag idea and some of the great stuff in .htaccess for easy gziping etc