My 2011, built for California, R3T had the CATs in the mufflers. The box is empty. The "box" you refer to is a design feature to help stop reversion back into the log manifold, due to the short header pipes. Especially the rear pipe. If the bike came with an equal length header with a collector, the box would not be required.
I would imagine the box also helps equal out the exhaust flow to both sides so, unlike a Harley, most of the exhaust does not go out the muffler closest to the header pipe exit.
Might I suggest reading "Scientific Design of Exhaust and Intake Systems" by Philip H. Smith. This book will explain the purpose of the "Box" right after the header "Log pipe" exits. The "Box" provides no back pressure. You will waste your time replacing it.
