I know that a naturally aspirated engine losses approx 3% of its power for every 1000 feet above see level, so how much of this loss is prevented with the EFIs?

I know the EFIs can automatically change the fuel/air ratio, but I am assuming there is still a loss of power at higher elevations. If so what kind of loss is there?

I am interested if anyone has experience with a Frontier with the EFI vs a Conquest at altitude.