I guess I'm still not getting it. It seems to me the restricted intake is the same as the throttle not being opened much relative to load. If I remember right, for the same engine output, the Atkinson cam timing has fewer losses than a more closed throttle.
For me, altering cam timing by re-indexing the existing cam would be much easier than increasing compression. But really, both need to be done to get the most benefit, or maybe any benefit at all. I'm hoping to get some benefit from the reduced compression by using operating conditions that high compression won't tolerate. Things like hot air intake, more advanced ignition timing, higher load, lean fuel mixtures and a denser cheaper lower octane fuel blend.
For efficiency, we need to match the power output of the engine to what is required. So the engine output for you depends on your driving cycle. We also must consider that the engine may not be most fuel efficient at 100 output, but something less. Injected closed loop motors obviously do better in closed loop mode than open loop, so about 75% or so of maximum. Carbureted bikes tend to be a little rich at full carburetor flow to keep the engine at a safe temperature, so not running 100% is probably a safe bet here as well to keep engine longevity reasonable.
My commute will have high speeds 75+mph for over an hour, temperatures in excess of 100*F at times, some steep climbs, elevation between 2500 and 3500 feet. It will be an unusually high power demand commute. Still, my 108hp bike is over powered. Any reduced output through delayed intake closing will not be missed provided an increase in fuel economy is realized. I could probably tolerate up to 50% reduction in power output.
Here is a somewhat confusing explanation and diagram of the intake timing modes of the prius. What do you make of it?
Prius tech training
So maybe running atkinson timing is not good at near maximum output?