I believe the large hole that is plugged, 377678-S, is an alignment hole for the rear quarters.
The holes were drilled with a hole saw if it had backup lights.
Looking at the clearances, the hole would have to be made either before the panel was installed or before the gas tank (and suspension) was installed. I think a drill might have the possibility of going thru the rear quarter, so a hole saw would be a better choice. The 65 Electrical does not indicate method, only an approximate location with the cable.
If the hole for the backup lights were going to be made today, I would put a piece of 1/2 to 3/4 inch plywood between the drop-off panel and quarter panel to "protect" the panel.
Jim