IIRC, the smaller black plate is to connect another black piece of plastic to the CD model 2 itself. Genesis model 1 units will stick out a few inches on the CD model 2, so Sega had another small piece of plastic that would connect to the CD model 2 to support the Genesis model 1.
This is probably very confusing, so I'm going to try to find a picture.
EDIT: [img width=530 height=323]http://www.gametrog.com/GAMETROG/HOW_to_connect_Hook_Up_SEGA_CD_2_Clam_Tray_Loader_to_Genesis_Model_1_a_files/SEGA%20Genesis%201%20CD%202%20d.jpg[/img]
The small black piece of plastic on the far left.