1) The only way I can figure that this works with apparently being so de-centralized and able to pull off a conspiricy involving some 70 people (The Founder Disease, figure estimated by Bashir)...is if Section 31 are like Masons or The Hellfire Club. 2) In "Extreme Measures"...what the hell did they do with Spoiler Sloan's Body? Call up Ross and say "Hey that guy who doesn't exist in that organization that doesn't exist? Come get him, and don't give us any shit about it."
1. It is de-centralized, they literally say it is. 2. Ross is a sympathizer. They also have nothing they can connect him too.