I think the easy answer is that professionals have a lot more time. A collegiate's schedule has to be more of a regimen with how a lot of other things in their life is more predictable. You know when conference is, you know when regionals is, you when nationals is, you know when mid-terms are, you know when finals are, etc. I am limited in the ammount of time I can spend with them as well per NCAA rules. As a pro, you can your life around your training schedule where as a collegiate it is the other way around. If you had a big workout as a pro, you don't have to workout again until you are completely recovered. However, as a collegiate there are meets and seasons that go by whether you are ready or not. So you have to be prepared to make the most of a schedule that is given to you in how you design stress/recovery around other aspects of their life.
In short:
pros = more intense, more time to train, more time to recover, freedom of schedule
collegiate = tighter schedule, "life stuff", you have to sometimes squeeze in workouts unfortunately
I don't like Magness too much anymore because of how he carries himself. His training is fine and he along with Canova got me really thinking about hill sprints/developing max speed in distance runners.....but I just haven't liked interactions with him. I need to get to know him better I suppose. However, if I would have to criticize the training aspect, I think his event specific workouts are not specific enough. He seems to gravitate towards pace alterations a lot. That kind of training is not as effective IMO. Having reps with a more consistent length/pace helps the body deal with the steady accumulation of lactate that you would experience in your event. If you are worried about not being prepared for surges then get fitter. The guy who fartleks all his workouts doesn't necessarily mean he is the most prepared for it in a race.
He also eventually lets go of a lot of the stamina work in his 5k plan which I don't agree with. He keeps it around once in awhile known as an "aerobic refresh," but I believe that it has to be done more frequently than what he suggests.