This is a very good point. Merging file changes between applications is not a trivial task and usually applications just end up saving their own copy (as you mentioned).

For example, if I share a photo from the Android Gallery app to Instagram, add some trendy filters and share the modified photo in Instagram, I end up with three copies in the filesystem: The original, and two copies made by Instagram to preserve both the original and filtered version.

After all, Instagram doesn't know/care whether the photo came from a camera or from another app, so it always saves a copy of the original.

Also, each time I share the photo to Twitter, Facebook or other cloud service I create another copy with different resolution, (re)compression and even dimensions, which is saved to the service out of my reach.

I guess having multiple unsynced copies of the same information is a problem that won't be solved as long as we want to have the ability to distribute information freely. One interesting development would be better content-based matching of files (e.g. Google similar image search, content-based indexing of photo subjects in Google Drive).