Usually the dealer will test the fuel to determine if it's bad and then blame the part failure on the fuel supplier. Sometimes it just happens though and parts fail.
I haven't done any "emissions updates" so my MPG is still decent. My driving style/route has changed a little bit as I'm doing more city driving during the week as I moved closer to work.. I'm averaging around 34 though even with the city driving. I've still hit 40+ on all highway trips.
It's likely the tune is conservative due to EPA guidelines on Nox output, etc... we all know, the more power, the more technology that's required to clean up and make it meet emission standards. Ram probably felt like they found that "Happy Medium" area.