Re: STAR TREK INTO DARKNESS - Grading & Discussion [SPOILERS]
Well the transwarp transporter was a secret weapon developed by Khan, only a few people including Scotty would really know the concept behind it and it was not widely available.
Transwarp beaming was a concept developped by Prime.Scotty in the future and told to Alt.Scotty by Prime.Spock. Section 31 just appropriated it and Khan used it.
And that's my opinion.