These are fine points, but if we factor in the probability that researchers carrying out these studies took them into account, we don't need to ignore "almost all dietary advice in this vein."
If a researcher designs a great experiment, but after collecting and analyzing all the data comes to the conclusion that there is no link between eating chocolate and health, then she will a horrible time publishing it in a respected science journal, even if that's what the data says.
Since journals want to publish interesting articles more than boring ones, and articles that are likely to be cited more often than articles without follow-up results, there is a bias against accepting negative results. As scientists are judged by the number of things they get published, and the number of citations their papers get, they have every incentive to only publish positive results.