I guess those "screws," Shimano part #Y8FA16000, are officially part of their tire-guides. I've seen plenty of posts quoting Shimano's own words describing them as "wear indicators" useful to prevent damage when using deep-section carbon rims. They are certainly there on both my DA 7900 and DA 9000 brakes.
But I agree, who knows what those "3" and "2" marking on the pad holders are.