Although the article seems to be on the money, it does not highlight that many (most?) of the clinical trials fall far short of what the average person would consider adequate.
Often the trial groups are quite small and the duration of "long-term" often is what most people would call "short-term".
Then there are the quirks. I remember one study (Gardasil or its successor, if I'm not mistaken), that only considered adverse effect that arose within two weeks of an injection - even though the vaccine itself was said to not take full effect until a number of injections over 18 months.