The tripod mount receivers on many video cameras have an additional slot next to the 1/4-20 threaded hole. This hole is for an alignment pin that orients the camera in the right direction and also assists in preventing the camera from twisting on the plate.
The holes in your Manfrotto 200PL quick release plate are for an alignment pin that fits into the additional (non-threaded) hole in the base on video cameras. The two holes in the QR plate are to allow the user to choose front or rear orientation of the plate when used with a video camera that has the hole for an alignment pin. Your Manfrotto 200PL plate should have been supplied with such a pin (they're typically black plastic, but were originally metal a LONG time ago) as well as a 3/8-16 to 1/4-20 adapter bushing for the main screw.
At least a few Nikon "still" cameras also seem to have a hole for the alignment pin. The Nikon D850, for example: