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.
You greatly overestimate the care one judge can muster about the prison system. They are complicit at best, and we have already seen a couple judges convicted for sending innocent 'customers' to private prisons in which they held stock on from which they received kickbacks.
Not that those things haven't happened, but this sounds overly cynical to me. Yeah, the bad part is that the system tends to be dirty, and sometimes does very dirty things to people who don't have the money or influence to fight it. On the other hand, if you have money for lawyers, or any influence with the media or politicians, then dirty tricks like that tend not to fly.
You'd have to ask a lawyer, probably one who practices federal criminal law, how such a thing would actually work, but I'm going to guess that if your problem is that the BOP keeps transferring you endlessly, then a lawyer could make a case for filing some kind of suit in almost any jurisdiction, and so you can take your pick of judges and courts.
