The pilot holes in the pump body are large enough for the core of the screw to be inserted, but small enough that the teeth of the screw bite into the pump body material.
In contrast, the clearance holes in the pump lid are large enough that the screw passes through the the lid without engaging the threads. In other words, while holding the lid away from the pump body, you should be able to slip the screw through the lid without any resistance. Of course, the clearance holes must not be so large that the screw head also passes through.
The following images show the relative sizes of the clearance hole and pilot holes, and the before and after relationship of the screw to those holes. Note that when the screw is installed, the threads do not contact the walls of the clearance hole.