Around the city it's hard to beat the low parasitic loss manual, as long as you're not dragging the engine along at high rpm (although some people like a "responsive" cruise, and this kills their mpg somewhat), as there's no hydraulic system to power, and idle consumption is lower (although if you shift into neutral it's almost even and if you turn off ignition when waiting at lights and stuff then it's the same).
On the highway you're stuck in 1 gear more or less, so it comes down to the gearing, and an automatic transmission usually has a longer gear for a variety of reasons related to fuel economy. I'm guessing manufacturers make the highest gear shorter on a manual because they assume 1. manual drivers want a "sporty" feel 2. no one can be bothered to downshift 3. no hydraulic pump gives them slightly more room in terms of fuel economy.
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