This directory of para-states is not a list of terrorist organizations, and is not constructed to supplement or complement the list of terrorist organizations of the US Department of State. The guide intentionally casts a wide net, and includes both the nasty and nice.
Although somewhat out-of-date the list is valuable because it really makes you ask (again) why Bush chose to prosecute a war on parastates by attacking the state of Iraq. The Afghan situation is different because al-Qa'ida and the Taliban had become so close that they were effectively operating as a single entity. That is why so few opposed Afghanistan and so many opposed Iraq.
Equally important, the list establishes that there is not one, but a whole constellation of jihadi parastates. Destroying al-Qa'ida would be an excellent thing. It would not necessarily prevent attacks by other parastates like JI or Salafiya Jihadiya.