Really, Section 31 is the Illuminati of Star Trek: anybody with any ambition at this Evil Overlord thing will claim to be one of their agents, or even their very boss, just for the prestige and notoriety. For all we know, the organization never existed, or only existed back in the ENT era - it's just a convenience and an excuse for all sorts of nefarious activity in the later eras.
Probably Marcus just gathered a team of like-minded Starfleet officers, organized them around a specific Starfleet Intelligence office, and told them to do his bidding under the S31 name. A dozen other cabals might have existed simultaneously, each claiming S31 identity or ancestry, and many working at cross-purposes to Marcus' cabal. (And perhaps, just perhaps, the real
S31 watched it all happen from a safe distance.)