I thought you had to use a nutsert if you wanted to mount something on the shell. For example in the rear above the lift glass.
A response by you to a question in May 2013 "Drilling through the rear wall panel above the hatch back shouldn't be a problem. You will be drilling into a cavity so you'll have to attach to it using an insert or pop rivets. Make sure you seal the area with silicon or neoprene to avoid water entering the cavity.
The rust you are seeing around the hinges is most probably coming from the torsion bar. The torsion bar is heat treated steel so it rusts, nothing that can be done about that. The sleeve that covers the torsion bar varies from unit vary in length, some are loose and some tight. The tight fitting ones can trap water inside them so it's best to drill a couple of weep holes in the sleeve to allow for drainage.
The hinge area does need to be siliconed. Remove any old loose silicon refill the area and make sure you seal from the hinge to the shell. Apply the silicon with the lid closed and the open. Open and close applies different strains to the hinge and opens up different areas that need to be sealed. Use a good outdoor rated silicon.
The area around the hinge needs to be checked and siliconed on a regular basis, at least every six months. "
On the main shell you can drill right through and put a backing washer on the inside.
I just want want to make sure I do it right when I develop the guts to drill my Flippac : O