Question: Is the "Eyes Only" qualifier a real thing, or did Hollywood make it up?
AFAIK, there is no actual "FYEO" qualifier. There are qualifers like NOFORN (No foreign nationals), NOCONTRACTOR (what it says on the label), and FOUO (which makes it exempt from FOIA). I see a lot of LES, FOUO and SBU data in my daily work, with the occasional Confidential and Secret stuff too. Top Secret stuff within the Bureau is usually handled at the SCIF, which I don't have access to. (Alphabet soup FTW!)
Pretty sure Nadaka could give a better idea of how it works on the DoD side.
A ton of stuff was de-classified during the early-mid 2000s regarding CIA Cold War activities in South America, especially clean admittance to involvement in Pinochet's rise to power. Most of this was roughly 30 to 35 years after the fact. I specifically remember reading a bunch of analysis from Chomsky on some critical information that had just been released regarding this stuff somewhere around 2005 or 2006, but I don't remember exactly what that information was.
That sounds about right. Political situation in the 1990's probably meant that it got an exemption at the time. By mid-2000s, South America was no longer as much of a strategic region (and many of the US folks involved had either died or were long-retired).
EDIT: Oh, and just for the WTF factor, the highest level of NATO classification is "COSMIC TOP SECRET". UFOlogists have had a field day with that for years.