My trunk lid was trashed by the previous owner - put 17 holes in it to mount a replica Saleen spoiler. I picked up a used trunk lid with four spoiler holes in it off Craigslist, then dropped it off at my preferred body shop and they filled the holes and painted it brand new.
If the light hits the trunk top at just the right angle you can barely see the repaired areas in the clear coat - doesn't bother me at all, looks great.
Obviously this is the more expensive way of going about it. If my original trunk lid weren't in such garbage shape, I'd have gone the plug route as well.