One problem I see with a setup like that is debris collecting in your collection box. Tree leaves, bugs, and birds tend to wind up in stacks and at least with the pipes, I can rev the motor and blow that stuff out. The box will have too many places for things to settle and get trapped. I would go with a Y-pipe of some kind in the bed and then make a box to shield the pipe. If you can be religious about putting caps on your stacks when not in use, you will probably be ok.
If you're wondering, yes I have had a to launch a bird carcass or 2 out of my stacks. It's kind of funny to watch feathers float out of your pipes when the truck is idling.
