Hm, basically, what you want is first: a way to tell MusicBee which files you consider duplicates, e.g. same tag metadata but different type; or same audio fingerprint, for the paranoid. Second: a way to tell MusicBee which file among any given set of duplicates is to be considered the "main" file; e.g. given a FLAC and an MP3, the MP3 is the dupe; given three AAC files, the two with the lesser bitrates are dupes. (As a logical consequence, you'd also need a way to tell MB about exceptions, in case it comes to believe a file is a dupe when it really isn't.) Three: a table (actually, two separate but linked tables) view with "main" files left and their dupes right, where unduped files don't show up.
The rest can be done with existing features. Use the new UI to review your possible dupes, reorganize the dupes somewhere else within the library and add a library filter to hide these "recognized" dupes.