Nitrogen dioxide is a problem, but at an industrial scale it's not a huge problem. Among other things it can easily be captured with fractional distillation (water, CO2 and NO2 have very different boiling points), converted to nitric acid and sold.

And aflatoxin (and others) are not byproducts, they are deliberately made by the organism, regardless of what it eats. A byproduct is waste that depends on the food source.