There would pretty much be no other opportunity for anyone else to handle the box other than a FedEx employee. Looking at the tracking, it basically went from hub to hub to local office to truck. The longest it sat was at the FedEx hub in Newark, NJ (13 hrs). Once it got to the FedEx in New York, it took all of 19 min to get on the truck, and was delivered shortly after to me.
It was clearly stolen. There would be no need to peel off the labels containing the serial numbers from the white box (picture 2) if it just wasn't packed. Stealing it would be easy, but someone spent a bit of time with the box to scrape off labels. That takes a bit more effort.