To be fair, the authors do acknowledge these limitations of their methodology, and these kinds of studies are a useful part of the overall enterprise of science to explore and propose hypotheses.
> First, we cannot entirely rule out the role of confounding in our observed associations. We controlled for multiple lifestyle and dietary covariates that might confound the associations of interest, although residual or unmeasured confounding, or both, may still exist owing to the observational nature of the analysis.
Regardless, I'll go ahead and take this finding as a further justification to keep eating dark chocolate.