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Are you talking about the gas tank protector? I assume that's what that rubber flap is for under the car on both sides. It's right in front of the gas tank and the tank hangs down low enough there to get hit by road debris.
That would account for one of the holes, but the rear most threaded hole is there on my car.
That is what I was talking about - not sure if they are for the gas tank though but that is as good a guess as any.