The main reason people gut the stockers is so they look STOCK and (hopefully) wont lead to a voided warranty should a suby tech look at it.
It is a royal pain in the ass to gut them, so aftermarket is definitely the way to go.
btw, I bought an ERZ flex uppipe from ebay for i think 75 shipped or so, included gaskets. Quality is very good on it, only fitment issue is the 2 studs closest to the firewall need to be cut down a little bit as they are too long.