This is true, in that very few best practices are universally applicable and you should never stop thinking. The author is also totally right about people jumping on bandwagons and being cargo cult members.
So I'm not really disagreeing with him, but just adding that a lot of best practices actually aid your ability to reason through code. They can help to push repetitive things off to the automatic portions of your brain. They can help to make patterns in your code that are visible and familiar, so you can spend less time thinking about how to implement (or read) some simple thing and more time thinking about how the simple pieces fit together.
Which is not to say all "best practices" are great. But even the questionable ones usually have some interesting problem they are trying to solve that explains why they sprung into being. If a "best practice" is popular enough that it gets called a best practice, it's probably worth paying attention to and thinking about even if you ultimately decide not to use it.