We now Harrison is working for Starfleet ...
We do? For certain?
Has their been an actual confirmation of this from someone actually involved in the production?
I hope you're not basing that on Peter Weller's line in the trailer that refers to "one of our top agents" being responsible, because that's most likely referring to Noel Clarke's character, whom Harrison recruits in exchange for saving the life of the man's daughter.
If you're basing it on images of Cumberbatch wearing a partial Starfleet uniform... why? Didn't the original Khan also briefly wear one in "Space Seed", even though he most certainly wasn't working for Starfleet? Ditto, that non-Starfleet 20th Century Air Force pilot they had to beam aboard in "Tomorrow is Yesterday"? And the android Norman from "I, Mudd"?