The MOT checks for Carbon Monoxide and Hydrocarbons to make sure the Cats are working correctly and the engine fuelling isn't too far out of adjustment.
Vehicle tax is based on Carbon Dioxide, one because it is a 'greenhouse' gas for which reduction targets have been set across the world and secondly the amount of CO2 produced is seen to have a direct relationship with the amount of petrol used so you are taxed based on how efficient the vehicle is in its fuel usage rather than the toxic gases it produces.