The reason for the second security check after customs is b/c you have access to your checked baggage which could contain items not permitted in the airport / cabin baggage. For example you can carry knives in checked baggage but no chance of allowing this in the airport.
We have the same deal at PIT where the customs area opens up into the level below the general gates but after the main security area. You have to go through security to get out of the customs area.