There will probably be lots of opinions but here's my .02: 1) swap the deck
lid for a good one the same color, or 2) use a plastic filler called
metal-to-metal. Make sure you get all the rust out even on the
underside...sandblasting preferred. If you have spray equipment use one of
the epoxy primers and prime before you apply the filler, if you don't, well,
fake it with something else...call around for local opinions. Even minor rust
is insidious so do the best you can and topcoat asap. Primer will let the
moisture through to lay waste to your best efforts.
Good luck,

Ken Hunter
82 Westy 1.9D
84 Jetta 1.5D
89 Mitsubishi van