Going a given steady speed on a given Rocket 3 requires x amount of power; no matter if it has headers or open intake or any other engine modification. Simple wind and rolling resistance to overcome. And, if a header and better breathing intake improve efficiency, then the motor should consume less air and less fuel at a given speed. The Rocket is not harmed by 14.7:1 at a steady cruise. It can run at 15.5:1 at 10% throttle all day long. The R3 does run cooler and smoother below 2,200rpm at 13.5:1 or richer. But highway speeds are generally above that where adequate airflow past the exhaust system keeps the leg cooler and mileage is of more concern to some riders.
Many TuneECU tunes I have seen are not optimized for driveability nor mileage. Changes to the throttle position map, load map, and the transition settings between them can provide great acceleration, still offer peak hp, and maintain mileage nearly as good as stock. Of course statement 3 applies to us torque addicts that can't keep from twisting the joy stick so getting good mileage is as much our choice as it is dictated by the tune.