I wonder whether developing deadly toxins in the organism's body is always or usually a defensive strategy rather than a by-product.
Developing anything by the body takes energy so generally only useful products are conserved. If some sort of mutation caused an organism to produce some sort of by-product that also happened to be toxic to its predators, then that organism is more favored to survive. No species ever starts producing something with the intention of toxicity in a predator/consumer of said species.
These xenobiotics that the plant/animal produces then can either be selected for because they're useful in whatever pathway they are a by-product of. Or they can be conserved because then this by-product has a defense use, regardless of whether the pathway its part of is necessary. Or both could happen, it could be doubly selected for.