I separate my files in Syncthing into different shared folders that sync to different sets of machines, and put stuff that doesn't need syncing at all on my NAS. On paper this might sound more complicated but in practice for me it's a much lower mental burden.
The way I use it, it's a 1:1 replacement for the way I used Dropbox: a directory of files that are continuously synced across different machines, with a durable central copy that gets regular snapshotted backups. I understand that Dropbox has more features now, but that's pretty much all it was when I started using it; and the fact that Syncthing supports other use cases than mine doesn't mean it isn't a perfect fit for mine. Out of all my experience self-hosting ~replacements for consumer cloud services, it's probably been the most successful by far.