I don't think that anyone would take the results of this article as a statement of absolute fact. In the discussion they mentioned some more (better controlled) studies investigating the role of cocoa flavanols in "cognitive tasks". Doing any longitudinal study with humans suffer from confounders, biases, and poor design because we can't do controlled, long-term research on humans. You just have to take these limitations into account when you are interpreting the results and use any findings as areas for possible further investigation.