The most recent plot-driven abuse of the transporter concept was CumberKahn's personal device delivering him to the klingon homeworld after shooting up a few fed big-wigs in ST:ID. I guess Section 31 got hold of some gear from someone like Gary Seven's mates.
Well, let's see, no. It came from the previous film, Star Trek
(2009). Spock Prime brought transwarp beaming into the new timeline from the Prime Universe, where it had originally been invented by Mr. Scott. That it was the same transwarp beaming used in STXI was, in fact, stated in STID.
With all the powerful technology that Scott had had to deal with over the years, including the Triskelion device besides just Gary Seven's, it would have been less plausible if Scotty Prime had never gotten a clue.