The dimensions of the object are used for geometric calculations, for fire calculations that relate to the material use the material settings. From the FDS Users Guide, Section 8.1:
The thickness of the wall indicated by the OBST line need not match that indicated by the SURF line. The thickness of the material on the surface of the wall is dictated by the parameter THICKNESS. These two parameters are independent for each other, the OBST line describes the overall geometric structure, the SURF line describes the characteristics of the surfaces of the geometry which includes the thickness of the layers of materials applied to that surface.