Concat, what you're missing is BSFC, or brake specific fuel consumption.
You are correct in saying that your car has to create the torque needed to drive the car at a given speed regardless of tire size, but internal combustion engines are more efficient in converting fuel to power at certain RPMs than others.
So even though the engine has to create the same amount of power to move the car down the road at 60mph, it may do so more efficiently at 2000rpm than at 2500rpm, for example.
Now what is the best tire size/RPM combo so that you minimize both moment of inertia of the tire/wheel combo AND bsfc? That takes a some math and a BSFC chart of your specific engine such as the one shown below. (y-axis is MEP i think)
This specific engine (dont know what it is, just pulled a bsfc chart from google) is most efficient at ~2250rpm and 15bar MEP