Apple iTunes Match (and Apple Music) subscriber, with 23,000 hand ripped songs, only about 18,000 able to exact match by Apple, 5,000 are less common versions.
Also have enabled iCloud Music Library. Note these are three different services, and iCloud Music Library has been the most likely culprit for monkeying with your music, not Apple Music.
The combo of all three has deleted or auto-replaced exactly zero of my custom rips. I can use a series of steps (smart playlist to find matched songs, then manually delete that set) to shift to using Apple's high quality unprotected version, or not.
I wonder if the key to everything working as you imagine is the Match subscriptions:
http://www.apple.com/itunes/itunes-match/
If using Match, then after matching, manually deleting local, then re-downloading, you end up with a very high quality file without DRM that will continue to work fine and be portable, even after you cancel.
I'm not sure what happens if using only Apple Music without Match.
The linked article sounds a lot like the iCloud Music Library beta problems in July 2015:
http://appleinsider.com/articles/15/07/01/apple-music-users-...
And similar support experiences:
http://www.loopinsight.com/2015/07/24/i-got-my-music-back-at...