Here is my setup :
I like the idea of all bags being scanned with increasing level of security and any rejects being a definitive illegal thing, because if we put additional scanner after the rejected to double check if the content is indeed illegal, this mean that we are likely to not use higher security scanner for the clean output of the level 1.
Which imply that all baggage considered clean by the level 1 scanner might just require level 2 or 3 (specific or manned) scanners to detect the illegal content.
To make sense as a gameplay mechanic, illegal contents should have 3 level of detection related to the 3 level of scanners, any illegal detection should actually go through a manual search station to check the content of the bag (no need to push things up to police and stuff like that though) which can help dealing with false positive, as any false positive should result in a pissed off passenger (we destroyed his bag after all) resulting in reputation loss.
The higher tier the scanning station, the more time the scanner should take to scan it, after all a guy can’t analyze as fast as a computer, but might actually by observing carefully see thing that a computer can’t detect.
This would make setup with potentially multiples identical scanners (for throughput) a necessity if we don’t want slow baggage route, which would encourage the use of tilt tray and more elaborate setup.