They can see your flight, and check your customs slip against it. I am sure it is also checked against a no-fly/watch list by HSA, and a criminal database to see if you have drug convictions or standing warrants. I would imagine, although I do not know, that it checks against previous swipes to see if you have been searched or pulled aside in the past. I think it also verifies the validity of the passport itself.
They still manually look though it to check your visas for the countries you have visited.