General logistics, I guess. In terms of personal armaments, Khan was rather well equipped even in his Qo'noS exile, but he didn't have a means of transportation or a sensor array with him.
What you would do with a super-transporter would thus be beaming starships
across sectors. That is, vessels with warp engines replaced by super-transporters, but the other elements such as big guns, laboratories, holodecks and cargo holds still remaining.
This also relates to the Scotty-still-has-the-skills issue. What would our heroes do with a super-transporter? We've seen they have big trouble locking on to a target even with their regular ones (cf. the conclusion of the movie), so they couldn't use the transwarp transporter to imprison John Harrison. They could use it to go after him in force, but how much force could they pack on their belts and packpacks alone? Sending a starship would seem to be their only option of either delivering decisive firepower (as Marcus wanted) or snatching back Harrison.