TL/DR: Fixed, but not really.
Dealer called yesterday afternoon and said the Explorer was ready to be picked up. I had my wife's car at work, so I stopped by the dealership on my way home to settle-up and get the keys. Total bill after tax was $3158.62. They dropped the $99 inspection cost and reduced the hourly rate to their "standard" $129.95 instead of the $147ish I was originally quoted.
Repair documentation indicates they completed the timing chain repair, the carbon monoxide recall repair, and confirmed everything was operational with a 6 mile test drive.
Fast forward to this AM. My wife dropped me off at the dealer at 7:20AM, so I could get the Explorer and drive myself to work. Pulled out to the stop light, got a green left arrow and proceeded through the intersection to the sound of a massive boost leak and no power.
Pulled a u-turn at the next intersection and dropped it back off at the dealer. Took the complimentary shuttle to work this morning, and now waiting on another call that it's actually fixed. Not sure how they missed that on the test drive. All the electronics and HVAC was powered down when I started it this morning, and I heard the leak over the sound of my heater blasting and the radio on.

On the plus side, no P0016 code in the 6.2 mile drive since the repair.