Let me just for one second give them the benefit of the doubt.

Could the $45 be a way to pay for some extra manual screening? Maybe? Or do they not deserve any benefit of the doubt.

They do not.

From what I've heard, the no-ID process does indeed feature additional screening. I think the passenger would fill out a form and the TSA would cross-check it with their information. This was free prior to the new ID push, but since now people need a special ID to fly instead of using their normal one, I'm guessing they made the process cost extra to disincentivize people from sticking with their IDs and just doing the free manual process every time. I'm not saying that's a good thing, I'm just saying that this is probably why they decided to try this.