I think you are saying that if the same song exists on two different albums that you want to delete one copy but still list all songs for both CDs so you can play them.
Now, in theory you can do this by replacing the file with a link, i.e. a unix symbolic link or OSX alias. And this option does exist in Jaikoz but unfortunately not in SongKong, I didn't add it because not sure anyone made use of it.
With SongKong if you are album centric the Delete Duplicates function is more about deleting multiple copies of the same song within the same album rather than deleting a song that appears on multiple different albums. But you can choose exactly how duplicates are found, the help goes into more details.