I'm rather surprised . . . they let Ben order his deck after shuffling with that complete BS "pile shuffle" (note: it is possible to randomize your deck a little bit with a pile shuffle, but not the way Ben was doing it).
1. Ben shuffled his deck the usual way at least ten times before doing the pile shuffle (not to mention Jeremy also cutting his deck at the end)! There was absolutely no way he could have affected the order of the cards. It was well randomized and clean.
2. Pile shuffling is an accepted method for shuffling cards when mixed with other methods (just as Ben did it; although, to be absolutely fair, it would have been better if he did the pile shuffle first and then the conventional one). Pile shuffling separates cards that might otherwise stick together, making randomization more thorough. It is not much of an issue in Netrunner, but in Magic, for instance, where lands usually end up in a group after each game, pile shuffle is a widely accepted way to break up these coherent grounps (again, when mixed with other shuffling methods).