I had a theory that any dust particles that might have found their way into processing solutions would tend to stick less to the emulsion if there was sufficient agitation, particularly during the beginning of fixing when the emulsion was still a bit soft. I don't know if it's true, but I have been very free of dust stuck to my negatives.
Speaking of clearing times for fixer, I always put a piece of cut film in a quantity of fixer while my film is in the tank being fixed and double the time it takes to clear. Is that sensible or overkill?
Constant agitation is fine, roller base agitation is fine, as is intermittent agitation, if you went at it violently enough I suppose you could stir up bubbles which might interfere with proper fixation locally. The idea in every case is to get fresh fixer next to the emulsion surface to ensure proper fixation.
If continuous agitation were a problem, JOBO would recommend removing the film tank from the machine during fixing. I've been rotary processing my film for almost a decade now with no problem.