This happened to me once, they just brought out someone (supervisor?) who asked questions about what addresses I've lived at, other similar questions I'd probably only know the answer to.

It does take longer than regular screening (most of the time was just spent waiting for the supervisor -- I'm not sure they were spending time collecting some data first), if that causes you to miss your flight you miss your flight.

It seems plausible to me that $45 could be about a TSA employee's wage times how much longer this takes. In aggregate, this (in theory) lets them hire additional staff to make sure normal screening doesn't take longer due to existing staff being tied up in extra verifications.