Also, resetting the database is not actually safe, and can easily lead to data loss and garble your share with conflicts.
In that case, wouldn’t it make more sense for the DB to be embedded into each .stfolder such that it’s tied closer to the files that they’re tracking? That would make moving drives/reinstalls safer as you don’t need to remember to back the syncthing database.
Also, other threads seem to imply deleting the DB is safer (ie How to backup Syncthing configuration and database - #3 by kluppy). Embedding the db in .stfolder would also solve the “delete the world if you add an empty folder” issue, since it wouldn’t be possible to have an empty folder AND a valid DB without someone actually deleting files.
Also you didn’t mention comparing permissions (or setting ignore permissions) - that might cause the discrepancy too.
Will check and get back to you, though I suspect they’re the same.