When it was first introduced in Deep Space Nine, it was an extremist rogue branch of Starfleet. It did not officially exist; was technically illegal; and many members of Starfleet attempted to capture it's members — but it was nevertheless protected by various powerful figures in the U.F.P. who felt it's continued existence was necessary.
Enterprise changed nothing about this and indeed Archer had never heard of it's existence and Section 31 sabotaged his ship and Reed was court-martialed for being a member.
Then in Into Darkness, it became a secret branch of Starfleet that was nevertheless completely legal, but most officers were not aware of it's existence.
And finally in Discovery, it was a known, fully legal branch. That Discovery also took place before D.S.9. made it all the more bizarre that most Starfleet officers in D.S.9. had never heard of the existence of an organization which was publicly known a century prior.