I live in base, and only commute occasionally for trips that I pick up in other bases that are better than the ones in my base.

Personally, I list for the earlier of the two flights, and then take a screen shot the day before to show that there are seats open on 2 flights. If I don't make the first one, I will automatically be rolled to the next one. I had this happen once. I called the crew scheduling supervisor and told her what was going on and that I didn't want to list for 2 flights due to AA's policy, but I listed for the earlier one. She took a look at the loads and gave me a positive space seat on the second one so I would be sure to make the flight.

I don't know what normally happens, but as long as you are not screwing around with the company, I think they will see it for what it is. If you only list for the later one, and do not call until after you miss it, they will likely burn you. If you list for the earlier one, and then get rolled to the next one - just call before you miss that one too.