Those are the tops of the holes for locating "spring pins" that precisely locate the HP pump into the gearcase. If you pull the HP pump, you'll see the little split pins driven into the gearcase. Not to worry!
EDIT: As Benny noted, when the cover is cast, those holes are rough and smaller than necessary. A finishing step is to drill those holes from the underside to finished size, but not all the way through the cover; what ya are seeing is the end of that rough, too-small hole . If you were to look at the underside, you'd see a fine finished hole probably 3/4 of the way through the cover. Don't take it off to confirm !
EDIT: If you pull up the Gear Housing parts, you'll see the little pins on the pump mounting surface. They serve to locate the timing shims as well..