I think Transwarp beaming is on ice with the augments. But they didn't need to use it at all. They could have said prime Spock erased the equation after they beamed aboard Enterprise in ST09. And Scotty forgot it. Or how about never mention it again.
If any of JJ's team monitors this board, don't try and fix things like this in future films again. It causes too much trouble. Just act like they never happened. For example, I haven't heard about Genesis since ST:TVH.