...has been miserable by modern standards, only 30-40 years as recently as two centuries ago.

When considering what's "natural" or not, please realize that long, healthy lives well into our 70s, 80s, and even 90s, is a wonderfully unnatural thing, not a realization of any basic nature. Our longest lifespans have corresponded with our creation of an increasingly unnatural environment. This is hardly to say that everything modern is healthy -- far from it -- but that, on the whole, the negative aspects of modern life that are mixed in with the positive ones can't be all that hugely bad if they haven't even come close to negating the gains.

If specifically apples harbor no worries in long term use, many other things from bananas to zucchini might. Or they might all be perfectly safe in normal use, but if you tested them the way artificial additives are tested, in huge doses and unrealistic concentrations, the same fears could arise.

The only advantage it makes sense that so-called "natural" foods would intrinsically have (once you jettison the mystical appeal of "nature" is that they perhaps have a slight edge in being more like what our bodies have evolved to tolerate. Two things diminish that edge: (1) A far wider variety of foods drawn from all over the globe are now part of our diet, as well as many new pre-GMO foods derived from selective breeding, making even a diet composed purely of "natural" products far more different and diverse than what human evolution has had time to significantly adapt, and (2) Since very few humans have ever lived and reproduced beyond their thirties, or even their twenties, during most of human evolution, there has been little significant selective pressure from what we'd now call "long-term effects".