there's also a paradox operating with an aftermarket exhaust: in order to sell them, the maker might want the buyer to
believe it will improve flow via scavenging effect, tapering, etc. (possibly legitimate claims) -- but many mfr's also claim their units don't require rejetting! (so they don't lose a sale to "ah, screw it, i'll stick with stock and avoid the hassle...")
well, to avoid trouble in the longer term (if you're the mfr), the exhaust had certainly better not make the bike perform noticeably worse, right? nor should it skew the mixture too far one way or another, affecting mileage, burning valves, and so on.
and what was honda really after with that sticker on the swingarm, "altering exhaust may affect performance, blah, blah"? on the one hand, they know what they're doing, and you can't go wrong with stock pipes. but if they guilt you into buying their pipes a few times, the sticker's pretty much paid for itself, hasn't it?
if you remove the baffling, yes, your pipes are theoretically less restrictive to the exhaust gases within. but they may restrict where, when, and how comfortably you can ride if you sound like a bazooka. by all means, give it a try.....

use the force, luke.
-jc