Your dealer is blowing smoke up your posterior, but then that's a pretty common thing with Harley dealerships. If the only thing you're changing is the mufflers, the stock ECM can normally compensate for that small change in air flow. However, while a "tune" isn't exactly necessary to keep your bike from self destructing, it would be a good idea in terms of improved driveability. Rather than explain it that way, it's easier for some places to try to scare you into buying something.
I assume this is a California dealer, so I'm curious as to what they recommended. Did they try to sell you a SEPST? Or are they a little worried about CARB busting their butts for emission system tampering and therefore not offering any solution?
My advice, whatever you do, hang on to the stock mufflers just in case California starts cracking down on individuals. I'm sure the time is coming when they will do so, and it will make it easier if you still have the stock legal mufflers to stick back on the bike.
Jerry