Ok let's be real here, if we put the "pollution" taxes onto fuel and not on the design of the car, this problem, in effect, goes away. There is still the issue that high efficiency, usually means running the engine at high temperatures which generates far more NOx gases. We should be taxing the amount of fuel used.
Every engine and car produces different environment waste.
For example a Tesla S produces much more carbon in it's production than a gasoline car. There are also other toxins which are produced concerning different type of cars.
A diesel produces NOx but can reduce it with filters.
Just taxing the fuel used is just stupid.