I think that's all evidence based medicine can really do. It's just a series of "well, people with high blood pressure tend to die early" and "people with high cholesterol have heart attacks". I don't know how they would approach it differently - if it was assumed that everyone was different with entirely different baselines, I don't know how it would be possible to make any sort of predictive assumptions. Really, the best solution would be to increase the granularity of the samples, but that's all they can do, develop more diverse pools of generalizations.
My kid was an outlier because my genetics tend to being tall and thin. If he was being measured against a set of healthy people with similar genetics he would not be considered an outlier - but this calculus is not considered when he is measured and judged aberrant. Our doctor being Indian was able to see from her experience that he was "normal" - for a kid with an Indian parent. Another doctor (like all the ones I grew up with) might not have the same insight and conclude there is a problem.
It's a problem that's been recognized in medicine for a very long time. That's why formal definitions of terms like disease and disorder usually aren't based solely on variation, and include a requirement that something actually interferes with a person's ability to function.
This has been recognized in medicine and mental health for so long that I don't know if you could find someone still practicing who wasn't taught it in school. If you go to a mental health care provider and tell them that your family thinks you have a disorder because you prefer not to socialize and get everything you need delivered so you don't need to leave the house again after work, they're going to ask you if you're unhappy about it or if you feel your life is diminished in some way by an inability to leave the house when you want to. If your kid has six fingers, a doctor's concern will be whether all the fingers are developing in a healthy way or one needs to be removed because it isn't functional and will be a source of pain and injury.
The principle hasn't been a panacea for prejudice, of course, notably in the case of homosexuality, but difference itself is not automatically treated as pathology in the absence of social prejudice. Doctors aren't treating people for having red hair or 20/10 vision or thinking stamp collecting is fascinating.