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In my opinion its still restrictive. The exhaust will swirl around in there causing a little back pressure. I've done it both ways, EGT's were a little higher with it also.
I've done it both ways, straight pipe and stock system and I can't tell any difference performance wise either way. The turbo whistle is nice without the muffler, but it is a much quieter ride with it on there. I'm running a 3" DP into no cat, and the balance of the stock system right now. It sounds pretty decent IMO.