I see your meaning, and this kind of confusion is exactly why Section 31 is so tricky to put in a story. It’s a secret handshake club, which may well go to the highest levels, but it doesn’t have official paperwork. There are likely varying levels of being in the know. Certainly many high ranking members of Starfleet know of S31, but opinions may vary in a sliding scale from “actively partaking in it” to “knowing it exists but choosing to look the other way” to “hearing it exists but assuming it’s mostly overblown rumors”.

Nobody is going to FOIA request the Section 31 files from Starfleet some day. That’s the difference between it and “CIA but in Space” that modern writing treats it as.