Even if we consider that, if the Black Badges in season 1 were indeed there to guard the Spore Drive, why did they completely disappear after Context is for Kings? Since Disco was then using the Spore Drive as a tactical asset against the Klingons, there would be a greater necessity for specialized security officers to guard it instead of telling them to pack up and see ya in your story arc next year.
That's just it - why are the guards there originally? Because Starfleet does not trust its own in wartime, and probably rightly so, as Lorca's crew is one of intellectual screwballs, weirdos who study mushrooms or worse. The ship is running experiments to win the war, and the Spore Drive one is not a leading candidate when Lorca kidnaps Burnham. The folks two decks over studying the viability of Purple Matter or Cosmic String Knots might be making better progress, but they mustn't know about each other - for the same reason Stamets and Straal were split, but also for the better reason that if Purple Matter bombs are to be deployed, these mushroom charlatans cannot be allowed to spread the tale.
But then Spore Drive pans out, and suddenly the ship has no need for personnel who would
not know what these black alerts are all about. Indeed, the giant vessel only sports a hundred-plus folks from then on. There is no need for internal security from that point on: S31 is not needed for fighting back Klingon boarding parties, as every starship by default has a perfectly regular security force for that very purpose.
That this overall would be a S31 project, no doubt recommended by Control at that, is hardly in doubt in retrospect (and no, don't confuse this with "writer intent" or other such irrelevancies!). Heck, Lorca no doubt sits where he does because he sleeps with the S31 heir apparent: Spore Drive (among others being studied aboard the
Crossfields) is likely to have been rather directly overseen by Cornwell, which is how this Mirror Man was able to land on his feet and start plotting a course back home. But S31 would not have a hands-on approach to the project as such, and Lorca would want those hands off, and would get what he wants because, well, Cornwell. Hence all these easygoing science weirdos being so surprised when S31 does get its hands firmly on stuff relating to their line of work again...
As for VIP guards, the one VIP I could see lounging behind that door is Cornwell. Given her overall omnipresence and duplicity, she's the one superior officer who would not get too curious about Lorca's elaborate plot to kidnap Burnham, and might actually be deeply involved in it. But given her behavior in her introductory episode, she'd have to be even more duplicitous than otherwise seems (i.e. a better actor even vis-á-vis the man who abuses the relationship with her)... I gather Lorca just pulled the wool over her eyes thick enough to keep her off the ship until "Choose Your Pain".
Timo Saloniemi