How does funneling pilots through the screening line do anything to prevent non-pilots from dressing as pilots? Real pilots ride as passengers, in full uniform, all the time.
I expect the reason is even simpler than you suggest; a total lack of exceptions to the screeing rules makes for simpler screening, simpler training, fewer chances to make mistakes, etc. And it's easy.
It doesn't prevent non-pilots from dressing as pilots. It just means (ostensibly) that even if you can pass as a pilot, you can't bring shampoo on the plane.
I expect the reason is even simpler than you suggest; a total lack of exceptions to the screeing rules makes for simpler screening, simpler training, fewer chances to make mistakes, etc. And it's easy.