A Stage 2 power setup consists of an aftermarket downpipe and a "Stage 2" ecu reflash. You wouldn't want to use a Stage 2 map on a car with a stock downpipe.
You could get protuned with your stock downpipe on, but you probably wouldn't be able to crank the boost up terribly high. Why are you so concerned with keeping the stock downpipe on?
I haven't heard of anybody altering their stock downpipe to increase flow. You could probably grind just a tiny bit of material from the opening or cut out one or both cats, but any gains would really be pretty negligible. There are a variety of aftermarket downpipes available and plenty of different ways to get them inexpensively if that's a concern. Almost every aftermarket downpipe will be lighter in weight and flow more air.
07 WRX (Albins 5MT + Blouch 20G)
Jorge Carrillo Tuned (365 whp/340 wtq)