You're forgetting about the JFK Limo being flown back to DC aboard the C130. If you believe the SS did Not get inside that car during the long flight back to DC, your gullible beyond belief. I believe this is when this bullet was found.
Strange, that pieces of JFK's skull would be found and immediately marched into the autopsy room for fitting into the holes in his head. Yet, there was No Mention of this bullet while Humes et al were X-Raying JFK's body from head to toe amidst the search for a missing bullet. No, not strange at all. Humes was snooker'd.
The protection detail, Landis included, flew back to Washington aboard AF1. I can't say positively that no SS agents were deployed to fly back to Washington on the C130, but I see no reason why that would have been done.
If the bullet was found during the flight of C130 back to Washington, it could not have been CE399 because that was found at Parkland.
What reason would there have been to send a bullet found in the limo to Bethesda during the autopsy. The skull fragments would have been important for the prosectors to look at, not any bullet or bullet fragments.