I compare the duplicate playlist to the original by creating a smart playlist:
If the duplicate has no songs that are not in the original, I delete the duplicate playlist. I've found that for some original-duplicate pairs, the duplicate has a few additional songs. Usually that's because I got tired of them and deleted them on the original; but I may drag them to the original. For other pairs, the duplicate has no songs that are not in the original. Conclusion; iTunes creates a duplicate during syncing whether or not it will include different songs. (I don't check for an original that has songs that aren't in the duplicate, because I buy my music on my Mac; so that will always be the case.)
I think the underlying issue is that iTunes was originally designed to treat the iPod/iPhone/iPad as a dumb appendage of the Mac. But now the system is evolving into a peer-to-peer relationship, and a playlist can be modified both on the computer and on the phone. So, during syncing, the software may be challenged to merge the Mac and iPhone playlist versions. One might propose various rules; generate a new playlist that has all the songs from the other two playlists; or take the playlist with the most songs as the master, or the one most recently changed, or the one that resides on the Mac. One might offer a choice of playlist syncing rules in Settings or Preferences and let us decide. Apple seems to have declined to face the issue, and instead preserves both playlist versions with no examination of them, saying basically that you're on your own. Which may reflect another underlying issue; Apple has become more interested in renting music than in selling it.
Another interesting wrinkle I've noticed in this business is that, after I delete the duplicate playlist, its entry in the smart playlist's rules turns blank. If I keep the smart playlist and sync again, and a duplicate playlist is again created, the smart playlist's rules don't show the duplicate playlist's name until I navigate to it, despite Live Updating. This suggests that playlists have system-generated internal identifiers. So, each successive duplicate of the same original gets a unique identifier even though its displayed name is the same as that of a previous duplicate. I'm guessing that Apple may simply be comparing playlist internal identifiers during syncing and not their visible names or contents. If the internal IDs match, you get a duplicate and it's your problem, not ours. Welcome to Apple Music!