Trying to be helpful here, they aren't covers over bolt heads, simply rest points for the topbox....I think.
If it's like the 650 the Suzuki plate allen bolts hold the rear handles too. The Givi plate is bolted down on a Givi base plate with the same bolts. The plastic adapter plate, seen in the photo, is held down with new bolts and square washers in the honeycomb grid.
Sorry if this is confusing. Do you have the mounting info ak007?