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gwern comments on Optimal eating (or rather, a step in the right direction) - Less Wrong
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The answer, as with most questions like 'why does X seem to work well for some people and not others' is going to be complex. For example, one of the recent links in my newsletter touches on this topic:
Aside from finding some hits, caffeine consumption has long had meaningful heritability estimates (some are cited in that paper, others can be found in Google Scholar with the obvious query 'caffeine heritability'). So that seems to be part of it: genetics.
Thanks for the paper (that's a lot of authors!). The complexity you mention makes it difficult to determine whether substance X (caffeine, alcohol, eggs, etc.) has a net positive or negative for any given person when it comes to health benefits. Coffee has been linked to some positive health effects, but maybe only for those people who don't get the jitters....that's the sort of thing that would be cool to know. Until then, I'm just going to listen to my body and minimize consumption.