If you want to sync playlists and only the tracks they reference, you now can.
Since some time between V2.5.5804 and V3.2.6827, Device, Music, '[] synchronise playlists' checkmarked includes not just the playlists but the referenced tracks too, so set '[] synchronize music' UNcheckmarked to exclude the UNplaylisted tracks e.g.

Devs, this now makes checkbox titles somewhat inappropriate. How about 'synchronize tracks' and 'synchronise playlists and their tracks'?