Because the intake valves of cylinder 3 and 4 are fully open, there is little to no restriction of the flow. In contrast, pumping losses are those that occur when the air has to pass the mostly closed, throttle plate. In an Otto engine, cylinder 3 would be sucking against the throttle plate.
With half of the intake stroke donw, now cylinder 3 is seeing some throttle-plate, pumping losses as the intake air has to pass through the narrow opening of the throttle. But unlike an Otto engine, this happens only for last half of the intake stroke.
During the power stroke, a 13-to-1 ratio, the hot gas expands releasing the heat energy into mechanical energy. This expansion ratio is not as much as a diesel 20-to-1 ratio but it doesn't have to be. In contrast, the diesel that has to compress the air 20-to-1 while the Atkinson only has to compress it 8-to-1 or less. These lower pressures and forces reduce internal, mechanical friction. At idle, both the diesel and Atkinson engines have a minimum fuel burn to overcome internal friction from piston ring sealing and moving part friction. The diesel still has to sustain a 20-to-1 pressure ratio, which means a fixed engine overhead. The Atkinson engine has an 8-to-1 ratio (or less depending upon intake valve closing.) This significantly reduces the sealing ring friction. Finally, the hybrid electric vehicle just turns off the engine at idle but that is not all that happens at low power settings.