Your argument loses merit when one considers that a vast majority of motorcycles are owned in addition to a normal car. They are not a the sole means of transportation for the owner.
Bearing that in mind, 100% of the "well to wheel" impact of such a vehicle is superfluous.
Precisely the reason why EPA has allowed for such relaxed regulations. If the market moved towards using motorbikes as a sole means of transport the regulations would likely be revised accordingly. Pretty unlikely to happen up here with all the white stuff.