I agree the resolution to this is to only mask the songs that cannot be deleted honestly, there really is not fix to this except for resetting your device and start over. I have spent hours on this deleting songs manually because they are NOT checked in iTunes but end up back on the device even though I have deleted them.
Either the iTunes on the PC is messed up or the iPhone's sync is messed. Regardless, I have read many posts and I see the same pattern here. I have found myself questioning why I continue to put myself through this pain and why I wont just migrate to android. In my opinion, iTunes has always been lacking features that I have wanted or features I have thought should be intuitive but not being able to wipe out your library is completely ridiculous to the point of accusing it to be buggy. I really think I need to evaluate my priorities.
Apple will you ever listen to your customers?