Currently, any new folder created under the Profile directory will be automatically shown in the Folder Tree, and user has to go to Preferences and explicitly disable it.
This could be OK in a perfect world, but in reality many programs tend to put junk here, and these folders can differ from PC to PC. So before syncing backups between machines, user must "collect" each junk folder from each PC and hide them in a "master-config". In only that way there would not be any unpleasant surprises appearing after syncing.
You could reverse that default behaviour, to make user explicitly include in the Folder Tree what it wants to see there (almost always that would be just folders like Downloads/Docs/Music etc. + AppData?). At least an option for that would be nice to have.