Of course, an aftermarket exhaust can really mess with the mix and torque curve (some bikes more than others). As far as the LT goes, I have not experienced any performance/behaviour problems with the Remus/Rhinewest combo. Mainly due to the fact that the chip has been tuned to match the fuel and timing to the exhaust velocities through the RPM's. Right now, its the only method I know of to do this on the LT as the PowerCommander never really panned out (The Motronic is a stubborn German).
Bottom line, just slapping on an exhaust rarely amounts to much except more noise and performance loss. Combine it with ECU tune and it MAY be worth it. I like the Remus, but to be honest, the performance increase was not earth shattering and I would not have done it if I knew then what I know now. It's a luxo-tourer and should sound like one, but that's just me.