Sorry to bring up an old(er) thread, but this might be helpful.
I followed this procedure on my 2.5i (thanks for the tutorial by the way)! Although I noticed similar wear as you on the metal portion of the rear shelf, adding the butyl mat and weather stripping didn't seem to fix the rattling I was experiencing.
It turns out that the rattling was coming from the airbag brackets vibrating against the shell of the car. You can sorta see these brackets in the second picture of Step II in the OP. I could duplicate the noise by bumping the plastic piece surrounding the triangular window. Gently pushing on the airbag cylinder would make an audible clicking noise, so I figure a higher frequency vibration would sound more like a rattle.
At any rate, if you stick some butyl mat between the brackets and the shell of the car, the rattling disappears! (I tried tightening the bolts at first, but they were already fully tightened).