The delayed closing has not been thrown away. Modern Prius engines use it to give a longer power stroke to a shorter intake "stroke" to extract more of the energy from the burning gases. (Think of the energy still available for driving a turbocharger.) The delayed intake closing effectively creates a smaller engine's intake charge while giving a larger engine's exhaust stroke. The quoted "Compression Ratio" is actually the "Expansion Ratio". The true compression ratio is close to an ordinary low octane engine's.
Why does Toyota use Atkinson cycle engines? - Toyota