Is there some way to get Emplode to recognize that two songs with the same path and filename are the same song?

Yes, don't use M3U files, use folders. Like here.

Unfortunately, it still requires that you do all your "personal mood playlist" editing in Emplode. I do this, and keep CSV backups of the playlists.

(Interesting trick. Did you know that when you copy a playlist to the clipboard in Emplode, it's in CSV format when you paste it into a text editor?)

A given song may appear on a playlist for a movie soundtrack, an album release and a personal favorites list.

For the movie soundtrack cases, you can:

a) Hand-edit each of the songs so that they're tagged, named, and foldered as their originial artist/albums and not as their soundtrack names. Then there's never any confusion.

b) Say screw it and just let there be duplicates in those few cases.

c) Delete the ones from the soundtrack albums where you've already got the original album.