Moved Journelly to sync only through Syncthing for now (using Synctrain). Only hiccup was ensuring Synctrain on the iPhone is configured to sync automatically (by default, it asks you each time if you want to sync files).
One thing I already appreciate: if there’s a conflict, it tells me, and saves the conflicting changes in another file, just like in Syncthing. Meanwhile, iCloud just “resolves” sync conflicts for me, and I have already lost important notes because of that.