Anytime that airport security (whether private or TSA or local police) go through your baggage, it should be done in front of you so that you can monitor it. You already know what's in your baggage, so why does inspecting your bag have to be done in secret in a hidden part of the airport?
Some airlines have baggage check/TSA inspectors' booths on the sidewalk outside of the terminal where you can observe them rifling through your luggage.
However, since you are not allowed to lock your luggage, any TSA agent can go through your luggage again, and again, whenever they want before it is loaded onto the plane.
I can think of a reason that makes some sense. When we left Mexico last month, authorities hand searched EVERY checked bag right at the check in counters. For those of us going on the TWO outgoing flights at the Alaska Airlines counter, the wait was over 2-1/2 hours we may have rather spent browsing the duty free shops (or just about anything other than waiting in line). Most people don't like having so much of their time being wasted for them - I know I sure didn't.