Yes, the cats are in the factory downpipe... That said, there is SOME power to be made going catless or high flow, but you MUST have a specific tune or you can actually lose a touch of torque not getting that back pressure. Personally, as in just me, MHO, I think it's disgusting not to at least run high flow cat downpipe, it's smelly and sooty and makes you look like a jerk all over 5 whole HP... Again, just how I see it... It's probably the most divisive thing among auto enthusiasts and I'm in the "run at least high flow cats" camp... I mean, the stock downpipe has like 800 cell cat converter, while at $280, you have the choice of Depo Racing 100 cell, or Whoosh 200 cell and those will cut the fumes to near nothing noticeable at least. If tuned for it, with all other bolt-on's already, you may make 15HP catless and about 10 high flow with a turbo upgrade, cut those numbers in half if only FBO on stock turbo.
And yes, what people call the resonator is what Ford calls the front muffler and what people call the muffler, Ford calls the rear muffler... Also, catless downpipes are known as test pipes in some of the other brand enthusiast circles.