I'm not sure the article author should be speaking with such certainty and authority on the subject of what constitutes "good" UI.
A lot of what makes interface elements effective is predictability. Context menus are boring, consistent, and predictable - or they should be. You shouldn't ever be in a situation where you right click on something and say "wow! that's beautiful! that menu is so amazingly well done!"
Software is intended to do things. If your interface gets in the way of things being done, then the interface is the wrong tool for the job. Making things flashy or prioritizing aesthetics over functionality for the sake of appearances makes every element you co-opt automatically the wrong tool for the job, regardless of how "pretty" it might be.
If your site takes over scrollbars, the correct response to "what do you think of the custom scrollbars?" should be "wow, I didn't even notice a thing."