Factory tuning is done the way it is for fuel compatibility, engine and component longevity, and a wide range of consistent performance at any reasonable altitude.

Changing the timing of the ignition, altered valve timing, and changing to a higher octane fuel can give you more power and better crusing economy at the cost of longevity, not being able to use a lower octane fuel, and possible issues if you drive at an altitude far different than the one it was tuned at.