I'd be interested to hear if someone who knows for sure could chime in as to what the best practice is and why. I can update the article to match.
In that vein, I think you're right that an isolate scope is generally a better default because it makes it clear that the directive expects no dependencies on the inherited scope, and it prevents the directive from overwriting any scope properties set by an ancestor.
I think using an inherited scope makes sense if you're building very app-specific directives that are tightly-coupled to their ancestor.
I used isolate scopes in the article because I thought they were easier to understand, but I'm thinking of updating it.