The ECU in these cars is a "learning ECU", it adapts to the tunings you do to the engine, as long as it isn't any major tunings. I work as a Toyota mechanic so i know what i am talking about.
The VVT-i kick that originally kicks in at 4500 RPM, does now kick in at 3000 RPM. There clearly is a kick at 3000 RPM as you can hear and feel the valves opening further, this was not so before i put the DE-CAT manifold and downpibe in the car.
As the engine breaths better the VVT-i can kick in sooner, it's as simple as that.