I’m interested, can you share some source for this information?
Such plants would assure to remove unpleasant substances in mature fruits, that are carefully designed to be eaten and to be as safe as possible.
Because different plant species compete for our attention. A plant that keeps putting harmful substances in its fruits is losing the game at middle term. We would just spread more seeds of its tastier competitors instead.
Tubers, bulbs or leaves would compete in a different league in that case
Humans indeed find some endogenous pesticides unpleasant; but we enjoy others very much, to the point of addiction. For example, nicotine from tobacco dust was used historically as a pesticide on other plants, and many modern synthetic pesticides are nicotine analogs (neonics). On a milder note, the compounds that give many herbs their flavor are also insecticides--it's easier to grow basil without an aphid problem than lettuce. The question of why we evolved to enjoy those poisons is interesting, with no clear answer:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817850/
That said, the original claim makes little sense. Natural pest resistance often arises from higher concentrations of endogenous pesticides, but this would generally just mean something like "stronger-tasting herbs", not any harm. Even if it were harmful, conventional growers prefer varieties with good natural resistance too.
This is not an accurate statement, obviously modern pesticides are not as targeted as would be optimal but they are most certainly not designed to kill everything by contact. For example I will apply Coragen later in the season when I need Grasshopper control, despite greater expense, because it is much less harmful to bees than more cost-effective options.