The modern interpretation of an Atkinson cycle design is keeping the intake valve open after the power stroke begins, allowing some intake gasses to flow back into the intake manifold. A number of engines use this strategy without advertising it, such as Honda's ubiquitous R-series engine (1.8L engine in Civics and such).
http://asia.vtec.net/Engines/RiVTEC/
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First, the intake valve closure timing is delayed to a very long period, way into the piston upstroke part of the cycle. The idea is to allow air to enter the cylinders freely, without using the throttle butterfly to artificially restrict air-flow. Then by opening the intake valves right through to the piston upstroke part of the cycle, the excess amount of air-fuel mixture that is in the cylinder will be expelled by the upward stroke of the pistons out through the intake valves and back into the intake manifold. When the amount of air-fuel mixture left remaining in the cylinder/combustion chamber is the desired amount, only then will the intake valves be closed. So instead of using the throttle butterly to control or limit the amount of air entering the engine, we allow the air to enter the cylinders and then push the unwanted amount out of the cylinders. So the exact amount of air we want is now controlled by the timing of the intake valve closure. In this way, the throttle valve/butterfly is not used/needed and it is allowed to remain wide open even under low-load conditions. This contributes to a a major reduction in pumping losses - up to 16% reduction according to Honda's calcuations. Combined with comprehensive friction-reducing measures, this results in a significant increase in fuel efficiency for the engine itself.
The new DBW (Drive By Wire) system on the R18A now constitutes a major and crucial part of the R18A's SOHC i-VTEC mechanism. Firstly, it provides the high-precision control over the throttle valve required while the valve timing is being changed over, ensuring smooth driving performance that leaves the driver unaware of any torque fluctuations. Secondly, and more importantly, during the economy mode there is the unusual, and conflicting situation where while the throttle pedal is at an almost completely closed position, the throttle butterfly in the throttle body is in an almost completely opened position, the exact opposite ! However, this relationship only applies when the engine is running in economy mode, when VTEC has activated the fuel economy cam lobes. In normal running, the normal relationship between throttle pedal position and throttle butterfly opening remains, i.e. light throttle means small throttle butterfly opening, etc. Thus the SOHC i-VTEC mechanism used in the R18A is only possible with a DBW system.
It's very much a multi-mode system as suggested by the OP. Honda's implementation overcomes the traditional disadvantage of a true Atkinson cycle design, which is reduced power density. This is why they are commonly used where an electric motor can supplement (such as a hybrid). But, as OP states, creative valve timing can effectively approximate an Atkinson cycle in an Otto cycle engine, and that is being used today in mainstream vehicles.
