UPDATE:
Yesterday, my wife received her passport. Our passport journey:
1. We had a trip planned Nov 15-17 to Quebec City, CA. We thought we might need to cancel, but took a chance on urgent travel processing.
2. Wife filled out the passport application PDF and printed it on 10/31.
3. Wife set up an appointment with the Boston passport office for Nov 5.
4. She took her application and hotel booking confirmation.
5. The passport office made my wife fill her parent's information. Wife thought this was an optional section on the online tool, but looking at the DS-11, it seems to be required.
6. The office made my wife change the emergency contact information. She had me down, but because we were travelling together, it had to be someone else.
7. She submitted the application, passport photos, copy of her MA DL, copy of her Naturalization Certificate, and the original Naturalization Certificate.
8. Apparently, even when presenting the original NC in person, they still keep it for passport processing.
9. She was told the passport and certificate would be mailed to her by Wednesday, Nov 13. She was offered the option of express mail (additional fee) for it to arrive by Friday, Nov 8. She declined.
10. The passport and certificate arrived by mail on Nov 7.