If Lifton was right and there was a big operation to hide JFKs body, do you not think they'd have been a bit more careful than to have Custer taking xrays of the body when Jackie and Robert came in with another casket. I mean come on.
Why? Bethesda was and is a naval facility. All staff were sworn to absolute secrecy on penalty of a court martial. None of the men, O'Connor and Custer included, said a word about anything that happened at Bethesda that day until they were released from their duty to remain silent when they were being interviewed by the HSCA, some 15 years later. Had that not happened, they probably would have taken the information to their grave.
And Custer never saw Jackie and Robert come in with another casket. They just walked through the main entrance after leaving the hearse. The casket was delivered to the back of Bethesda. Custer saw them in the hallway and had no reason to assume they had come with another casket.