Lots of discussion about this. Even stock I can typically hear when the MDS kicks in. The freer flowing the exhaust, the more you can tell, and for some people that is very annoying. I personally cannot stand drone, which the HEMI has always been known for, and I believe why there are resonators in the exhaust system.
Last week I had a local muffler shop remove the stock muffler and install a Borla muffler only. I can hear the MDS deactivate 4 cylinders slightly more, but I doubt a passenger would even know it. I know it, but it is not something I would say is annoying. The overall sound is really quite good. I have used Flowmaster on maybe a dozen cars and trucks over the year, but my local guy, who does the work, no longer like flowmaster. He feels they are over priced for what you get, and that Borla is just a superior product, often for the same money. His 2 cents. I just like the way my truck sounds now.