Going by the letter he linked, it sounds like it would make it much harder for the prisoner to contact and interact with lawyers, family, etc. You normally can't sent or receive letters or phone calls while in transit, since it would be a pain to organize and transit is normally short. If they could keep somebody perpetually in transit, though, he would tend to be isolated.
On the other hand, this sounds like a higher-profile prisoner with access to good legal representation. I would think that, if they actually tried to do that, the prisoners' lawyer would figure it out eventually, and a court would most likely take a dim view of such a practice.
I'm not sure if they've ever actually done that, though. It sounds like they might have kept some problem inmates tied up in pointless transit maybe for a week or three. Doing it perpetually sounded more like speculation than something they've actually done, or could realistically pull off.