I can't comment about other people's experiences with truck and box paint, except to agree with Linda's point that the rules change from time to time. Also note that FedEx Custom Critical's contract is an at-will contract, meaning that contractors can be terminated for any reason, or no reason.
I can comment about the Glen and Janice Rice truck pictured below. This truck was leased to FedEx Custom Critical for a while before it was destroyed in an accident. It was not something that snuck in under the radar. EVERYBODY at FedEx Custom Critical seemed to know of this truck, including the people who make contract decisions and enforce policy.
Notice the blue lines on the top and bottom of the box. Because they were there, the Rices were not allowed to display the FedEx Custom Critical logo on the truck. They were allowed to bring the truck into the fleet and run it with FCC. Their lease was not terminated because of the box color.
As Diane and I understand the rules today, we could paint or graphic design our truck body (box) any way we wished (within reason and good taste) while continuing to lease the truck to FCC. We just would not be allowed to display the FCC logo on the truck.