Look carefully at the URLs of two bookmarks which you think should be detected as duplicates but are not.  Bookmarks will only be detected to be in the same Duplicate Group if they have exactly the same URL, character-by-character, as explained in Removing Duplicates.  This is usually pretty aggressive, because our apps also normalize URLs when they are first entered or imported.

The one thing that our normalization does not do is to remove trailing slashes, and there is a reason for that, but you can do that with the Aggresively Normal URLs command.

There is no way to mark a folder as allowing duplicates.  Here are two alternatives which others have used to get close to what you want

1.  Ignore duplicates in different hard folders.  This feature is typically used if you want to allow bookmarks in, for example, your Favorites aka Bookmarks Bar to have duplicates which are elsewhere.  I think this is where you may have read that Preferences > General reference.  (The next sentence states that for BookMacster, the setting in not in Preferences but is instead in the document window's Settings tab > General.

2.  Use the multiple-selection smartness of our Inspector.  You can set Allow duplicates for all bookmarks currently in a folder by using the shift key to extend the selection from the first item to the last item, then when all are selected, in the inspector switch on Allow duplicates.  The setting will be applied to all of the selected items.

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Not many people use these features, so let us know if any of the above does not work as you expect.