Why is the current Sonic series so different from SatAM? What happened to Mobius and the Freedom Fighters? Is SatAM “official” or “canonical?”
In short, yes. Throughout the 90s, Sega maintained different versions of the Sonic mythology for different territories. These basic storylines branched off further into alternate universes in the comics, cartoons, and publications created by each region. SatAM played a particularly prominent role in the west, as its characters and story were an evolution of Sega of America's own mythology and were adopted by the company itself.
When Sonic Adventure debuted in 1999, it drew heavily from the Japanese game mythology—much to the confusion of fans in the west. Sonic Team in Japan now sets the standard internationally, and most licensed media conform to the universe portrayed in the modern games (with the notable exception of Archie's Sonic comics). That said, the prior continuities are no less official, legitimate representations of the character that hold a place in the larger Sonic "multiverse."
See the Feature article, The Great Sonic Continuity Debate for an in-depth discussion of this topic.
For more on the Freedom Fighter characters check out The Evolution of the Freedom Fighters.