I just checked mine, no hole

Actually, that is not a hole. The material on the left side of the seam (drivers side) of your pic is folded upward. The material on the right goes down inside the body. There is an area that is split at the bottom of the seam. Water on the right side of the seam will drain downward on the outside of the material. Water on the left side of the seam (drivers side) will drain into the door, or will drain downward onto the right side of the seam.

Water would practically have to travel horizontal and upward through this seam separation to work it's way into the interior of the car. Even if a drop or two got in, there is no carpet back there and it wouldn't hurt anything. I think this may be one of those idiosyncrasys.

After checking mine again, I found that the passenger side is sucked up nice and tight, while the driver side has a slight separation at the bottom of the seam. It looks normal as part of the design. There is rubber that is placed in such, that will cause the water to drain either inside the door or in between the outside of the top and the body on the right side of the seam.

 

That's what mine looks like