There was actually quite a bit of dialogue where Scotty questions whether these folks are Starfleet or not - and it appears they indeed are from a separate "security contractor", that is, mercenaries. Doesn't mean they would be the normal or intended crew of the Vengeance
; they are just what Marcus employs for his one unofficial sortie with the ship.
Yes, there was also (somewhat vague) indication that Scotty is surprised by the very existence of the Vengeance
, never mind her design specs and oddball crew and nefarious mission etc. But that doesn't mean the ship would have been built in secret. Secret from Klingons, no doubt, secret from Romulans, yeah - but Scotty not knowing about it doesn't yet mean she would have been built secret from the Federation.
Really, all that actually happens is that Khan gives Kirk an address for a dockyard, and Scotty checks out that dockyard. That Scotty is able to do so suggests that anybody
is, meaning the dockyard isn't particularly secret after all. Hell, it's deep within the Federation, at the very heart of the Sol system!
Basically, Khan just told Kirk to send Scotty on a dinghy to have a look at a particular dock at Newport News, something any fisherman could do from his boat, and does every Sunday. But while the fisherman would see nothing of interest there, the very fact of Khan giving pointers to that specific dock would alert Kirk and Scotty into taking a closer
look and realizing that there is more to that humdrum dock and its supposedly humdrum ship-under-construction than meets the eye.
All the rest of his appearances, he wore that leather number, as did most of the other S31 folks we saw.
Well, all other S31 folks we ever saw - namely, the background extras on the holodeck in "Inquisition". Everybody else associated with that organization was merely doing its bidding without actually being a member or paid employee, and even that list is extremely short: Admiral Ross and Julian Bashir. And out of those two, Bashir was faking it.
So basically we're still in the situation where Sloan is the only actual S31 member known to exist for real. That is, if his own feverish fantasies count for "real".