Modern turbo engines are a great example of this. If you drive them like the factory tester going for the EPA certification numbers then they get good mileage. But take that same car out into the real world where everyone drives like an idiot, get on the boost and it drinks fuel like mad.
Because to get the power out, you still need to put the fuel in. Sometimes over-boosting small engines makes it worse than that bigger lazy engine that never breaks a sweat.
That said, peak engine efficiency at a steady cruise is somewhere around 70% load. So theoretically the small engine is better.
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