You propably need couple of new holes into body and tailgate for the
parts. Clean and dry the area, drill in dry place and paint the exposed
metal. Water may find it's way through the new holes, I would use rubber
washers to seal. If the area later on catches rust, silica based
sealants may be difficult when you need to repaint. You are quite safe,
if you manage to prevent creating active (electro)chemical pair with
body/tailgate and new parts. Paint and sealant help in this. When
working close to existing throughs, do not break the seals in them.

Following is guessing, I do not have TJ: If you need to make holes into
interior trimming and water block (sheet of plastic) between trim and
body, at least make X like cuts into plastic. Similar when installing
speakers that do not fit between trim and the block.

Lock will bang to tailgate and frame, perhaps some sort of plastic or
rubber pad to prevent metal to metal touch and paint damage could help.

And if you plan to keep the vehicle for years, proper corrosion
prevention for the whole vehicle helps to keep rust at bay. At least my
California bought WJ came with very light anti-corrosion package, dealer
was more concerned on sun burning the paint :-) I have now
http://www.dinitrol.com/ based corrosion prevention (tuff-kote dinol)
applied.

   Marko