Depends where you draw the line. Any auto-pilot in modern America will naturally result in an early death. I'd agree that magic pill syndrome is self-defeating, but having, for example, the knowledge that oxalic acids deactivate alpha-amylase and interfere with starch metabolism might lead one to certain food pairings that would not have occurred otherwise. Similarly, drinking with a meal might dilute one's stomach acid and make digestion less effective or increase the risk of infection.
Do we disregard all acquired knowledge regarding eating simply because it doesn't mesh with our natural inclinations?
It takes me slightly more time to slow-cook my meat, but it tastes better to me and has fewer carcinogens. If it didn't taste better but was less carcinogenic, should I not do it because I could have spent that time playing tiddly-winks?
There are certainly a lot of hopelessly neurotic things that people do for longevity's sake that are either completely worthless or have strongly diminishing returns. There are a lot of things that are obvious though.
Eating doesn't get in the way of living; eating is living.