I guess? There's another note from somewhere else (and still on the Wookiepedia article) that Thanaton was in fact a Dark Council member for almost 40 years, which obviously makes no sense if you've played the game. It's another of those Game VS Comics cases, though Thanaton definately behaves like he's been in charge for that long.
Maybe he had some sort of pull with that particular project, or he was in put in charge of sorting out what Mekhis had left behind. Personally, I'm somewhat getting the idea that the concept of the 12 Spheres (or Pyramids) was not 100% solid when the game was released and it was not determined who was in charge of what and why. Most of the infos on that came from the Encyclopedia and perhaps there were different writes involved.
No, he didn't become a council member until chapter 3 of the game. In Blood of the Empire he was only given the title of Darth Thanaton.