I bet if you were buying Screamin" Eagle aftermarket parts that you were purchasing thru this particular dealer, they'd gladly install and support.
X2...Ask them if they would install an exhaust system that they normally sell, and would that be covered under warranty, and if so, what the difference is. I can somewhat understand about the TTS because they want to sell you the SEPRT, even though the SERT used to be built by the same folks, and the newer version (TTS) is virtually the same thing with added features not available on the SEPRT.
This kind of stuff is a dealer by dealer type thing...find another dealer.
Or better yet, put the Stage I on yourself, hook up a laptop with the TTS and upload one of Steve's canned maps. Save a few hundred dollars for about 4-6 hours of your own time.