When creating a prefab, you can deselect all selected metatiles and save a prefab with no metatiles (or alternatively, an empty prefab can be added manually to the prefabs .json file). Selecting this prefab in the editor will update the selection size, but painting with it does nothing. Creating empty prefabs should be disallowed, and they should be removed if loaded from the file.
When creating a prefab, you can deselect all selected metatiles and save a prefab with no metatiles (or alternatively, an empty prefab can be added manually to the prefabs .json file). Selecting this prefab in the editor will update the selection size, but painting with it does nothing. Creating empty prefabs should be disallowed, and they should be removed if loaded from the file.