Not a bad point you make there. Worst case the Varex Muffler is stuck closed and performance is hurt just long enough for me to get it to the shop to get it fixed or removed.
I've decided to go through with it though! I'm going to have my Greddy Revolution RS cut right near the rear axle and reroute it out of the passenger side exhaust cutout and have the Varex Muffler inline where the OEM muffler would be. Here's some quick measurements I took below for the way my exhaust is currently routed.