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Sure, but who has oversight over the long term stuff? Generals come and go. It just seems weird that some other person (or group of people I suppose) can tell a Prez "that's above your pay grade".
Most of the state department, intelligence community, and various bureaucracies are lifers who pay little mind to politics because they're too busy running the big machine. A president or some junior senator or a general can likely make demands, but it's not like they can follow up on it. If the secret to an alien conspiracy is in the hands of someone in Washington, it would surely be at the level of a senior person on the ground doing work, not some appointee.
All my speculation, of course, but it's not that different than working at a huge company. Guys running projects select what they share with their bosses in the home office, and pretty much keep them on "need to know" because they don't want interference.