No. This method of simulating a gate has no direct physical relevance. The effect of a gate is to shift the energy levels. In reality, the shift is very complicated and may be different for different levels and in different parts of the system. The "gated method" in ATK 2008.10 is a highly simplified method to describe this effect, where all levels are assumed to be shifted by the same amount. There is however no way to map this shift to a particular physical gate configuration. But the influence on the transport properties is similar and can be used to investigate how the system would respond to a gate.
In ATK 10.8, we introduced a realistic way to describe gates (and dielectric regions), where you specify physical gates and their voltages etc.