Yeah, that is what most seem to do and it seemed that the issue was the hump that goes over the axle is the problem.
There did seem to be some difference in the Borla instructions when it came to their louder systems (ATAK and Type S), where they don't say to cut behind the muffler, but I could never figure out why that would affect the stock removal. I just figured if I pulled the trigger on either the Borla or GM Perf, it would become clear what to do somewhere along the way of installing it.
Given what I have heard on the comparison clips, I don't think I would be reinstalling the stock in any case.