You might be waiting a while... it's rare that we reach a consensus here! Usually we agree to disagree and try to keep it friendly.
All kidding aside, the vertical section of the chair rail is the primary thing that holds the bus walls and roof to the floor. The exterior sheet metal attaches to the ribs in the wall, the ribs in the wall attach to that vertical section of chair rail, and the chair rail attaches to the floor. We can debate the importance of the flange the seats rest on, but the overall piece that creates the pocket where moisture is getting trapped (if I've understood you description correctly) has to stay.