I recommend that the rules be the main list and not the folders.
List all rules and add a column to show which folder(s) it is assigned.
Use a filter field to search for specific rules.
Then you can change one rule and have it work for all folders it is monitoring. Instead of having to fix each duplicate rule.
Since Hazel is about scripting rules, it makes more sense to me.
This would be much easier for new users. At first it does not make sense why you add folders first.