I know the feeling, but typically I arrange everything into a variety of folders using OPML files, so I’ve got sub-categories of my own OPML file that I import into particular folders for reading. As a result I try to only categorize each feed into one category (usually based on how often I read particular ones). Then there are others’ OPML files that I subscribe to (like yours) which go to their own separate folders. Often these I read more for discovery, so I just skip over the duplicate feeds (or rearrange the duplicates to the bottom of their respective folders to mitigate.) From my discovery feeds, when I find myself regularly reading particular feeds, I just move them to my own categories and derank them from my discovery feeds to mitigate the duplication.

It would be nice if readers recognized the same feeds in multiple folders and marked them as read when matching posts were finished. There definitely needs to be some work/research into making some of this manual work easier…