MA explains it well:A distinction without a difference.
- Unlike the Tal Shiar and Obsidian Order, it operated on its own, without Starfleet's knowledge or consent
- Its very existence was a deeply buried secret, known only to a handful of people beyond its own membership
- Only some of Starfleet Command's top officers knew for certain of Section 31's existence
https://memory-alpha.fandom.com/wiki/Section_31