I don't think just because someone says "Article 14, Section 31" we can automatically infer that the supposedly secret wing of Starfleet Intelligence we know as "Section 31" is automatically involved.
I have a feeling that for many of the Federations early years an organization called "Section 31" did not really exist. It was just a handy legalistic reference for elements of Starfleet to say "this is why we're sometimes allowed to do bad things for good reasons". The actual organization "Section 31" probably was just the group that adopted that name to glom themselves onto the way certain elements of the Federation had been doing things for decades thus giving it the aura of history, tradition, and legitimacy.
I have a feeling that for many of the Federations early years an organization called "Section 31" did not really exist. It was just a handy legalistic reference for elements of Starfleet to say "this is why we're sometimes allowed to do bad things for good reasons". The actual organization "Section 31" probably was just the group that adopted that name to glom themselves onto the way certain elements of the Federation had been doing things for decades thus giving it the aura of history, tradition, and legitimacy.