The Platform Keyboard Tray features two different height settings which allow for different clearance options. The standard tray setting offers 4.25" between the tray and desktop, while the lower setting offers 5.375" clearance.
Looking at the two wooden tray wings you'll see two silver L-shaped brackets that attach the wings to the desktop. To lower the tray, remove all of the screws and attach the bottom two screw holes of the silver bracket to the top 2 holes on the wooden tray wings (which will leave two holes exposed and unscrewed).
Please see the image below. Simply shift the L bracket in the direction of the arrows so that the green dots are where the yellow stars are. Once you've done this, you can then install the tray wings underneath the desk as you'd do normally with the regular tray setting.