You could put a small barrier behind the insert so the bondo does not get any further down the hole.
+1
Tighten the screw deeper than it will be when the joystick (or bracket?) is installed.
Use a bit of tape to block the hole.
If you're worried about bondo working past the tape, seal the edge of the tape to the side of the hole with clear nail polish.
If you need clearance above the insert, pack some cotton around the screw to support the tape. After the bondo dries, you can pull the cotton out through the insert using needlenose tweezers or a hook made of wire.
Scott