What exactly is supposed to go in the under deck tray in a 23/24 Prius Prime?

The uppermost right and left corner squares are where the deck board slots into. Not sure about the middle square. The other two spots on the upper left are for the socket if you have wheel locks and the longer slot is for a centering stud if the car had come with lug bolts instead of wheel studs like was originally planned.

If you go to bolts(like most European cars), it's hard to hold the wheel in place while starting the first bolt. So they give you a hard plastic aligning stud. You push or thread the stud into the hub and that gives you something to hang the wheel on while you get the first bolt in. Once four of the bolts are started, you pull out the alignment stud and replace it with the final bolt. Between the preproduction cars and the regular production ones, Toyota decided to switch from bolts to studs(because of the bolt problems on the bZ4X) and then the car no longer needed the alignment stud. But the design of the foam deck boxes was already set, and it wasn't worth it to modify them to remove the slot.