I am actually running my Berlin Classic on a mag 9.5. I also use a mag for my return, and I have never had anytype of rust problem. I just recently took both of them apart to clean them out, so i think I would have seen something if I had a rust problem (OR wouldn't I?)
By cutting down the center tube, you are making it easier for the bubbles to make it to the collection cup. One of the many problems with this skimmer is that it uses a "triple pass" configuration, so basicly your pump needs to pump the water up the length of the skimmer, down the length of the inner tube and then back up the length of the inner tube. By cutting the tube back a little, you take out some of that length. You do loose some contact time, but it is a trade off. I have not done this mod, but I am often considering it. Before trying, I would replace the inner tube with a peice of PVC so that you can try a number of different lengths, before cutting the acrylic.
I figure, that this mod would not be necessary if you used a bigger/better pump.
Honestly, with the Mag 9.5 and the replacement venturi it will pull out a lot of sludge from your tank. The big problem is consistency, as you constantly need to tweak it. If you don't adjust it every couple of days, it will stop pulling anything out of your tank.