Something this article brings up and that you touch on is: coupling your use of CSS3 to JavaScript being enabled.
There is an incorrect way of using Modernizr where you always surround your use of a CSS3 feature with a `.feature .box` class, which is generally unnecessary and leads to the issue the author was concerned about.
Modernizr classes are best used in the `.no-feature` case, where you do something like use background images or another clever CSS use to mimic the feature or handle the fallback situation. In general I like to code my styles optimistically though.
I left a comment on the site saying it's hard to address this subtlety of the "right way" to use Modernizr classes. We're launching a new site very soon and hope to better document this approach so people don't go down this tricky road. :)