Yeah..heltonjk is right..
on the manual.. when you shift.. you lose rpms and while youre doing so.. you lose boost.
on the automatic... there's a sort of blow off valve (correct me if i'm wrong in the description of that thing) that keeps the boost up while the car's shifting.
I suppose you could probably build up the turbo setup.. to not lose as much boost while shifting... with added components and what not... and get the manual shifting version.. as fast... or faster...
but stock.. the auto is faster.