The holes in the body should be just wide enough to let the screws pass through without catching at all. If not, they need enlarging.

For the tightest neck to body fit, the screws should only actually screw into the neck. If they are screwing into the body and neck, there's no guarantee that when the screws are tight against the body, that the neck is pulled down as tight as it can be. So the holes in the body there are primarily there for location. You don't want the holes too big, as that allows the neck to shift if it gets knocked; just big enough for the screws to slide through snugly.