From what I've read, it serves two purposes. One- to program new remotes and Two- If the battery in the remote goes Tango Uniform, you can remove the door key that is in the remote to open the door and then you would place the remote in the small molded area to start the truck.
And there used to be a nice hidden storage compartment there in the 2016's and before. I don't get why they had to complicate the system with this. I had someone explain that for ranch trucks, you put the remote in there so you don't have to hand a key fob around -- anyone can jump in and drive off. It's part of why Ford has always held onto the driver's door keypad.
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