Trust me, the problem is not in my library. But over the years I've used a series of services, and I'm not limiting myself to my flawless FLAC library nor my vinyl collection. The Rush example is actually a real example from Spotify.
Also, adding two checkboxes or the ability to customize the way the sync is done hurts no one.
Im not talking about changing the behavior but adding options.
OK, and I'm saying that IMO a bunch of phantom plays in the library because a user ticked those options without thinking through the possible unintended consequences is a worse outcome for the end user than missing a few plays from unsupported third-party sites like Spotify.
The behavior exists here to mimic last.fm's behavior and also the experience of iTunes, etc, which is to track each time you listen to a specific track on a specific version of a specific album either on mobile or on the desktop. If you click any scrobble in last.fm, that's what you get, and that's what gets brought back into MB.
The intent is not to keep track of how many times you've heard a song in any context in your lifetime. Luckily, the last.fm API gives you the ability to do that as you've discovered, but that's not the behavior people expect from their library software.
Not trying to be overly argumentative, but I do feel this would be a damaging change that goes against expected behavior and conventions across multiple library managers. IMO, as always.
A smile is happiness you'll find right under your nose.