The first distinction here should be what kind of "code" are we talking about. As far as I see there are two main possibilities:

  1. code for performing a scientific simulation or analysis (a script).
  2. code for solving a specific problem generally (a program).

There are different "best practices" for the two situations above. And the article primarily talks about applying "best practices" from the 2nd scenario to the 1st. Of course they don't apply.