Ok new update. Idiot alert idiot alert. I'm such a stupid idiot. The antenna is fastened to the spare tire trim under the floor board. When I removed the spare tire, floor board and large piece of plastic trim that surrounds the spare tire for my apparel rack the passive entry antenna disconnected. I had no idea. I didn't unhook it. When I removed this huge piece of trim I didn't see any wires so when I pulled the trim out it disconnected the harness. So later on when I saw the wire I thought it was for something else like a pre-wire for a hitch. Duh.
Needless to say I put the dealer through 3 trips of trying to fix this thing. So when they called me today asking about modifying the back sure enough they were right. However, they didn't say the antenna was fastened on the large trim surrounding the spare tire. I could have easily looked and found it. So sitting and just thinking about the entire ordeal and wondering where this black box was I just had a hunch to look on the trim. Sure enough there it was. It blended in like a hunter in the woods with camo gear on.
I feel obligated to call the dealer and tell them how bad I screwed up. I feel even worse because I sat there face to face telling the service manager there must have never been a black box (antenna) ever installed from the factory. They never challenged me.