That is the first thing that came to my mind. If you want more power in an internal combustion engine, you must put more fuel through it, you can do that by adding capacity, or forcing in more, using charging.
Problem is, you do use more fuel to make more power, and more fuel put in means more fuel burnt, means more emissions put out.
Now, let's say you drive both your single turbo and dual turbo at the same speed, then you should use the same joule energy to do that, given the gearing and some other factors are the same. Why then should there be a significant emission level difference whether you have a single or dual turbo vehicle. Not sure, as you should use roughly x joule to perform that work - given both vehicles weigh the same, have the same aerodynamic qualities and same gearing, etc.
This makes for an interesting topic, but I suspect we need a serious engineer to bring a conclusion.
By increasing the efficiency of the engine I.E. increasing the power output for a set amount of fuel by reducing other losses such as internal friction, heat, noise and rotational inertia. At the end of the day its a balance between an efficient engine and one that doesn't cost a fortune to build.