I didn't realize I hadn't mentioned the program's name. I probably thought I was asking the question in its specific forum or it would be obvious which program it is. The product in question is ThinApp (Capture). I don't think that version is relevant to this question.
It's only a suggestion. I know it isn't a common thing. Not even compression programs check for duplicate files when they build an archive, and I know it is a feature more commonly found in setup authoring software, because it is most often obvious to them which files are duplicates. It is however possible to store duplicate files only once in ISO disc image files (a feature called "optimize" by most disc burning applications), which are a kind of archive as well.
So why not in ThinApp (when building output). I can think of several situations where one packages software from the same developer, which may have duplicate DLLs and various resources in each of their programs' folders. The idea is to decrease the size of ThinApp's build output.