Yes, it absolutely does matter. The screw heads need to be at, or just below the surface of the hardibacker. When I say - at - I mean they need to be flush. You can check by running your hand across the area and feeling. If the heads are sticking up, the installer will be able to tell, because the tile will not set down evenly. They will need to pull the piece up, and since you used screws, they will need to try to get them down below the surface of the hardibacker.