Step 3 is to simply compare your boarding pass and with your passport. As noted, in step 1, the contract security staff simply look at the boarding pass. The passport reader in step 2 reads only the passport and your thumb, but cannot reconcile with the BP (which the real ICA agent does for real people, i.e, foreigners).
I once quizzed the step 3 person to see what she was actually doing, and I was told to just move along quickly, but I insisted and a supervisor came to explain. Apparently it was not done when the machines were first used, and perhaps some people ended up in the departure lounge without a legit ticket?