Every once in a while, something goes wrong at the gate (e.g., during irrops), and the GA starts collecting paper boarding passes. With the ones printed at home, the GA just tears of the corner that has the sequence number on it. That's all they need.
The other day, auto-check-in on the return flight gave me #2. On the outbound flight, I checked in at T-24 and got #221. I suppose pretty much everyone else was connecting and checked in earlier than T-24. Or they all were on their return, and auto-check-in had already run.
Now that time of check-in is no longer a significant tie-breaker, it doesn't really matter anymore.