The programs are typically geared towards getting the biggest dyno numbers possible on the given fuel choice. (usually the highest octane pump gas you can get)
If you want to optimize fuel economy over performance, they can tweak the timing to retard things and let you run a leaner mix and sacrifice performance. The SCT multi tune chips can be switch with a switch from one tune to the other. So you could have one for fuel economy and low octane fuel, then another for racefuel.
Other things people ususally have done, clean up idle, change the engine fan temp settings so they come on earlier so you can install a cooler thermostat. Then also remove speed or rev limiters, or set them higher.