Well, the rubber plugs are to plug the holes, certainly not the drain holes. One pair is to plug the holes you marked, the other is to plug some other holes. One pair of the holes, as per the plug description is for paint to get to certain parts of the chassis during the immersion painting process. The other pair is to plug the holes made for some other purpose. There are several purposes the holes are made in the chassis - they are technological holes - for painting process, for installation of something, for rust protection application, etc.