These seem to be pretty routinely granted, even to political advisors with no prior security/foreign policy/intelligence background, such as Karl Rove. If the President says he wants Joe Blow on his staff to get a Top Secret clearance, I assume the FBI will at least interview people who know him and make sure he has no prior felony convictions, but is that about as far as it goes?
Has any top White House aide ever been denied a security clearance? I sure wouldn’t want to be the FBI agent who had to tell the President that his college roommate, whom he wanted to appoint as counselor, senior advisor or the like, is a dope addict or a spy for the Chinese.