I just looked at mine.. Those cut outs towards the rear are NOT for "covers" so nothing is missing.. I have nothing there. (never noticed, as its right by the seatbelts and because of the seat, not really visible) and mine is stock.
I IMAGINE they might be for heat, since it does get a bit toasty under there in the front, and MAYBE for transmission of the heat to the rear... but there are no "covers"
What you have there is stock, except for the carpet on the side missing and the center painted black (should be wood grain) and exactly what I was looking for... If you want to sell it, or find another one in the treasure trove you found, give me a shout.
-Gonz