Sequece of events:
Scotty Prime perfects his transwarp formula after his TNG-era resurrection. He tells Spock Prime.
Spock Prime goes back in time and shows Scotty. Scotty and Kirk beam from Delta Vega to the warping Enterprise and later Kirk and Spock beam from the Enterprise (over Titan) to Narada (over Earth)
Section 31 confiscates the equation from Scotty, and builds the portable transwarp beaming device. Khan steals it and beams from Earth to Kronos.
With Section 31's R+D facility beneath London destroyed, I think the formula's been lost. It's only in Spock Prime's head, now.