Well the way the "gate" works is to move the Fermi level of the atoms you project it on. So if the HOMO-LUMO gap is large, moving the Fermi energy has no real effect. Besides, the Li-H2 system is a toy model so it's hard to extract any real physics from it...
What you can use the gate for, for a more realistic system, is to simulate the effect of a gate (naturally) the influence of which is to charge the central region (positive or negative).
Also note that in ATK 10.8 you can insert real metal gates and dielectric screening regions, allowing for a much more realistic gate electrode effect.