I assume we're talking about diesel?
Aren't diesels only tested for smoke anyway? I imagine poorer quality fuel will be more smokey, so that might be something to consider. Even supermarket fuels made my old remapped mk4 Golf smoke more.
I'm not sure whether the emissions would be different or not, but regardless of that, I'd be more worried about the quality of it.
I work for a construction machinery dealer and we get diesel delivered into our tanks for filling the machines, and even though the diesel is white (a lot of customers can only run on white) none of our engineers will touch the stuff for their new vans. Even Tier4 machines are a concern when it comes to quality.
You'd need to consider sulphur and biofuel content.
Still assuming it's diesel, if it's ever had red diesel in it in the past then the filters will be stained red. The MOT won't check this, but if you live in a very agricultural area and you are suspected then you could get checked by another agency.
Red diesel has very high sulphur and will knacker a modern diesel engine, so any fines would be the least of your worries. A3's need ultra low suplhur diesel.
If we're not talking about diesel (red or otherwise) then forget everything I've said above