The latter was a proposal by a select number of men within the US government, and shot down by JFK before it could be enacted. US History is in no short supply of similar plots so as to come into conflict with other countries, and this rejected proposal is documented as well.
The former went so long in part because it targeted a specific demographic in the US that hadn't received its share of civil rights for most of the time this study went on, and too many didn't care about them especially in 1960s Alabama. Then civil rights and Vietnam flooded the public eye, so it was unlikely anyone would have thought anything was wrong, compared to usual for the state of Alabama in the 1960s, until the whistleblower came along and inevitably unveiled the whole thing in 1972. So yes, this was almost an exception, but it's also no secret that blacks were mistreated and not given proper care in this country. I suppose it's like hiding an aging plutonium-based weapon inside a hill of garbage for a few decades, and someone finally pointing it out when new regulations for said garbage enter the works.
Keep in mind this is only what has been uncovered and declassified. I think you'd be naive if you think something like Operation Northwoods is the only plot the CIA has cooked up just because we know of its existence. If you read about something like that and you don't forever distrust the CIA and our government as a whole after that then I think you've got your head in the sand tbh.
Basically, your logic is that the CIA only ever tried something this nefarious this one time and it was stuffed by JFK and they've been relatively above the floor after that