Just keep in mind that if you skip the check in counter there is a chance that you will get stuck in a doc check lineup at the gate.
I skipped the check in counter at AUS, and then my SE status meant nothing to the contract agents at the gate doc checking what seemed like 100 pax. I had to get in the back of the line and wait. They started boarding before finishing the doc check and they sent J pax that hadn't doc checked to the back of the doc check line...so the next time I was at AUS I did the doc check at the check in counter.