Let's say you're missing some tracks you deleted from your phone the other day, but MB deletes those tracks from library too as soon as you connect your phone to PC. This could happen. Auto-deletion of tracks from library is already too dangerous a feature, and if that's combined with auto-syncing, it would do more harm than good whatever confirmation is set up.
You can achieve this by setting up some auto-playlists (one for all tracks in your device, the other with all tracks in library and a rule of "playlist is not the former one") and manually deleting all tracks in the second playlist occasionally.