The 2 disc set contains the original 10 programmes, as transmitted on TV. Together with a bit of unseen footage and a post trip interview, you end up with a total running time of 315 minutes.
The 'Special Edition', 3 box set is a 'director's cut' which includes all of the material that the director would like to have included if he'd not been constrained by the length of the slot available to him on TV. (At least, that's the theory. It might actually just be the production company's way of making a re-issued series seem more interesting). You still get the unseen footage and the interview from the 2 disc series. There's also an additional interview with the creators of the series. Putting all of that lot together takes the total running time to 600 minutes.
Chris