I was exactly that, SS.
The rationale for this security is apparently that
a) you are going to be mixing with passengers in the boarding lounge so anything in your luggage (which, note, could be huge backpacks which would never qualify as carry-on in a 737) could be passed to somebody else, and
b) you are going airside and could walk up to a 737 etc and sabotage it.
The first is trivial to address: get GA crews straight out to their plane.
The second is not trivial to address but in most places GA planes are parked so far away from jet transports that if you were taking the half mile walk you would most likely get spotted.
As I say, physical separation is the way to do this, and in most places it would be easy. Unfortunately, most airports are run by people with zero lateral thinking; they never realise that GA (business GA especially) could represent significant traffic if it was supported.