There are some tuners that are getting better mileage and better emissions on stock setups, but it's a one off tune per truck.
Custom tuning is where the tuning really is great these days. The box tunes need to work on 95% of truck, but a custom tune only has to work on one truck and support one set of mods. With custom tuning it's very easy to get better mileage empty and towing, and have more power.
The engineers have to deal with the EPA, since custom tunes don't the end user gets a better product.
At no time or use was my stock setup better than it is now, mileage, power, smoothness, or noise. I am right at the highest hp that Cummins ever made a 5.9 as well.