It seems to me that when they are routed out the back, fumes seem to draw into the cab easier than when the pipe is routed out the side. I would run it out the side, personally, but if rocks are a problem I could see running them straight out the back.
I used to have a Chevrolet Astro van back in the day when I installed satellite dishes and home security systems. It had a bad head gasket, or something... All I know is that it blew out bluish smoke before it finally died on me. Have you ever seen a vehicle with a blown head gasket running down the road? No matter what, the back glass gets caked in oily, filmy residue... that should tell you, right there, that the fumes will kind of rotate up into the cab of the vehicle with rear exiting pipes. New cars/SUV's may have corrected this with better weather stripping and tighter seals, but fact is, fumes will get into our beloved EB's should you go the rear exit strategy.
I saw your post on broncoholics... Broncow had a pretty good idea with his post... if you don't mind cutting up your rig a tad, that'd be a perfect solution for a dd/rockcrawler, IMO.
Good luck, either way and let me know what you did! I've got to work on my exhaust pipes soon.
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