Secret adds an interview with questions pertaining to different things that could be used for extortion and a credit check. It boils down to a few things: are you a perverted removed; are you in the kind of debt where someone says they've got a job for you; and are you involved with any far right or left anti US government groups.

TS SCI adds a more extensive interview, fingerprint registry with the FBI, and multiple character interviews with people who've known you for a long time. Depending on the SCI compartment and or the resources available, you will eventually get a polygraph as well. The people who get interviewed also have their records run, and it's used to sus out if the affor mentioned interview concerns. They also check watch lists for your name and the names of your character witnesses.

All that is to say, none of this work checks your mental health, any of the nuance of your political beliefs, and doesn't touch on your personal convictions. The security clearance system just isn't meant to to consider this.