You should be allowed the stop over. I just booked an AE ticket from YWG-YVR-OGG and returning OGG-SFO on United with a stop and then onward SFO-YVR-YWG on AC. The AE agent at first said wasn't allowed but after a brief hold came back and said it was permitted. It's allowed in the 50 United States excluding Hawaii. I had to make my booking through the call centre as the web website won't allow it.