But the smaller engines still need to overcome almost the same wind resistance, tire and friction resistance, as a larger engine; and still need to push the same 200-350lbs bike + rider.
On a smaller (aka 33-110cc) engine, these frictions would equate a higher percentage of their output power than for a larger (aka 125-250cc) engine, resulting in less remaining output power to the wheels, and overall efficiency drops compared to a larger engine.
If both large and small engine where made with the same hairline tolerances, this would result in the larger engine being more efficient than the smaller one, as (to simplify
a 0.1mm tolerance on a 10mm piston head equates 1% tolerance, vs the same on a 100mm diameter piston head, equates to 0.1% tolerance.
In both cases the measured piston gap tolerances are identical, but the larger piston will have less losses than the smaller one.