Plastics burn really well, they are not actually that hard to destroy safely - their decomposition products are very clean if the fire is hot enough.
In short, "not actually that hard to destroy safely" is wildly off the mark.
Your other statement is wildly off the mark, too. Metabolic byproducts are incredibly diverse, including all of the chemical compounds produced in the course of an organism's life cycle. One of the organisms studied in this paper was Aspergillus niger, whose metabolism produces, among other things, aflatoxin. EDIT: Oops, WRONG. It's other Aspergillus species that produce aflatoxin, sorry. A. niger is mostly notable for producing 99% of the citric acid in your food.
The chlorine makes salt, and the fluoride can be sold to be added to city drinking water.
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.