IK in Seattle...I think you've nailed it. I've often done same-day return trips and only 1 E-Upgrade was deducted for the entire day's round trip. This was checking in with human units, getting all Boarding Passes in both directions up front.
I haven't experienced this Internationally yet, as I don't do turn-around Mileage Runs. But definitely U.S. Domestic it's happened to me. Many times.