Not even close. Smallpox is "designed" (over an optimization gradient) to attack our bodies. Although it would have been much more effective to not kill its host.

Showering is a practice that has likely had minimal selective pressure on our genes due to the relatively short history of the practice.

Yes, of course there are exceptions to every generality. Man also isn't conditioned to sit at a desk for 8 hours a day or eat highly processed foods on a consistent basis. This doesn't disprove his point that exposing yourself to a little bit of the natural environment is probably a good thing.

What? That completely disproves his point that "exposing yourself to nature is probably a good thing." You can't cherry-pick which types of nature you should expose yourself to -- you have to supply some other criteria.

Your analogy doesn't work because the author was not advocating experiencing death, just experiencing short-term discomfort that is supposedly better in the long run because humans could/should experience it. To use your words the author was indeed advocating "cherry-picking." Compare dying of smallpox to freezing to death in the Arctic Ocean. Compare taking cold showers to building up disease resistance by living in non-sterile environments.