Section 31 was portrayed less as an extremist cabal and more as a misguided morally-grey organization
My interpretation was more that they were “hiding in plain sight” at that point in time - Pike was under the impression that they were some kind of special forces, and learned the truth over the course of the season.
I only watched this trailer once, but I didn’t see any insignia, so I think S31’s exact status is still TBD.