I think so.  For bookmarks, not folders.  The feature to mark any bookmark as Duplicate Allowed is explained in the Help Book.  Since our Inspector now smartly handles multiple selections, an easy way to "harden" a whole bunch is to show the Inspector, select all of the bookmarks which you want to "harden", and then switch on the Duplicate Allowed checkbox.  It will affect all of them.

Note that if you only have two bookmarks to a given URL, and activate Duplicate Allowed on one of them, Find Duplicates will now find neither bookmark.  If you have, say, three bookmarks to a given URL, and activate Duplicate Allowed on one of them, Find Duplicates will now find the other two.

An alternative "shotgun" approach, which might get what you want, is to Ignore Duplicates in Different Hard Folders.