It is true that “conspiracy theory” is a loaded term, and can be used to attack an idea without engaging in reasoned debate. However, if we accept the idea of a “mainstream narrative” we must also admit that there are people creating alternate narratives for various unsavory reasons, whether it is to attract attention, gain influence, market extremely profitable YouTube videos, advance their own social causes, and so on. We have to be particularly suspicious of conspiracy theories that aren’t really falsifiable, but simply use well-deserved distrust of authorities to invent layer upon layer of additional explanations.
As to the link you sent, it is an interesting one. I believe that events like the Gulf of Tonkin “attack” and the CIA experiments with syphilis and LSD did real damage to our trust of authority in general and the government in particular, and it sparked a suspicion that fuels conspiracy theories to this day. Some of the other links are overstated or perhaps deceptively worded— the vaccine program that may have helped catch Osama bin Laden was exploited but not “fake” which is an important distinction, that rich people like to gather yearly and congratulate themselves is hardly a conspiracy, does taking money from the American government (in the case of the Dalai Lama) make you an “agent” in any meaningful sense of the word, and so on.
But I think the most important point I would make is that we risk a selection bias by considering only the extraordinary claims that have been proved true. If we were to consider all the ideas that might be called conspiracy theories from the past 50 years, we would certainly find that the vast majority were utter nonsense, as they are today. (I remember when I was young there was a viral theory about “spontaneous combustion” — a great number of people literally believed that a person could burst into flames for no apparent reason, and the authorities were covering it up. You certainly won’t find that on a list of “top 10 conspiracy theories that turned out to be true.”) Yes, it pays to be vigilant with the facts people present to you. But automatically adopting “alternative” arguments is going to lead you astray more often than not.