I think the file is simply listing the previous Sonic games that Sonic Team worked on. Sonic CD isnÃ¢â‚¬â„¢t listed because, although the box art carries the Sonic Team Presents logo, it wasnÃ¢â‚¬â„¢t produced by the exact same team members that worked on the other Sonic games. Interestingly, the bibliography file on the Sonic CD disc is blank.
This isnÃ¢â‚¬â„¢t the only time Sonic CD has been omitted from official lists of Sonic Team games: The 2004 Sonic Team quiz covered every Sonic Team game (including supervised titles such as Sonic 3D and Sonic R), but omitted Sonic CD (and the Sonic Team supervised Sonic Shuffle).
The "true" storylines of the Sonic games are of the Genesis originals, and the Adventure series, as those were all done by Sonic Team. I think SEGA and traveler's Tales were the ones behind stuff like Spinball, 3D Blast, R, and such.
It worth noting that the Sonic story line has changed over the years. Back in 1998, only games with a Sonic Team logo seemed to be a part of the story, but over the years other titles have been incorporated, including games that Sonic Team had no involvement with (such as Chaotix).