Aye, it is far better to close the intake early than late. Late closing pumps the mixture twice to no purpose at all. The best retrofit, and a candidate for OEM is a reverse supercharger - run the generator off the intake vacuum. That makes it easy to have a regular supercharger, but then it becomes very helpful to get a variable compression ratio to keep the actual charge density at ignition uniform. Perhaps the main bearings should sit on a series of ramps that can be cranked fore and aft.
Ideally, the exhaust valves should not release unused pressure, but we currently waste the intake pressure differential needed for that without a true Atkinson crankcase.
Lean burn is wonderful for efficiency - those NOX producing temperatures mean high Carnot efficiency. A stratified charge and some EGR help to tame it, but catalysts probably leave more efficiency.
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