I'd say the difference is two-fold. First, desktop applications generally still have unique icons and branding. Second, desktop applications have much more freedom as to how they combine the elements. Usually you can tell which application it is from a distance, because the layout has been designed to suit the app's specific needs and functions. The OS chrome itself is meant to be invisible, in favor of what makes it unique.
For example, Firefox, Safari and Chrome all look identifiably different on OS X, despite all implementing the same overall style.
Twitter bootstrap isn't just a CSS style, it's a rigid layout and UI pattern. The author is decrying the use where bootstrap is the only kind of design being done. In that case, people typically haven't considered what layout they want to use or which elements to emphasize and how. They just go with the standard 960 grid and its simple divisions, regardless of how much content there is, and take something that's meant to be invisible and emphasize it visibly by not adding anything new.
While bootstrap gives the appearance of being well designed, often the content inside it fails to live up to that promise.
For example, Firefox, Safari and Chrome all look identifiably different on OS X, despite all implementing the same overall style.
Twitter bootstrap isn't just a CSS style, it's a rigid layout and UI pattern. The author is decrying the use where bootstrap is the only kind of design being done. In that case, people typically haven't considered what layout they want to use or which elements to emphasize and how. They just go with the standard 960 grid and its simple divisions, regardless of how much content there is, and take something that's meant to be invisible and emphasize it visibly by not adding anything new.
While bootstrap gives the appearance of being well designed, often the content inside it fails to live up to that promise.