iTunes – Random Songs Appearing in iTunes Library After Activating iTunes Match

I think the difference is in the second paragraph that you posted. In your situation, if you have bought less then 7,000 songs from iTunes, then the rest counts against the storage.

In other words, it looks to me that only the songs that you bought from the iTunes store will not count against your 25,000 song limit. All other songs will (whether bought from somewhere such as Amazon, or ripped from a cd) likely count against that limit.

Keep in mind that you can have more than one Apple ID with purchased music in a library and according to the FAQ - only the Apple ID paying for iTunes Match/Apple Music is exempted from the 25k song limit.

It's not clear whether Family Sharing is all considered "one Apple ID" so you might want to be sure you re-download all family songs under your Apple ID if you are running up against a limit.

To detect incompleteness iTunes would need something to compare the track to. Unfortunately this is not available therefore you really are out of luck here and have to download each song individually once you find it by listening.