Using the same settings for Sync, I was able to confirm the behavior your describe with the foo and bar folders.
I’m finding that when items are moved from the draft folder to the trash, and then the external folder is synced, the corresponding items in the external folder structure are (as expected) moved from draft to trash. But if the trash folder is emptied in Scrivener, items in the external folder remain behind, but they are not brought back into S when it is resynced.
After syncing my main project just now, there are 4 items in the trash, but the external trash folder has 14 items.
After emptying the trash in S and then resyncing, the external trash still has 14 items, but the S trash remains empty.
Not sure how trash syncing is supposed to work, but it doesn’t seem as though the external sync folders, even just the trash folder, should be able to remain out of sync after being synced.