I think I finally got this working properly. I think it's still a bit complicated, but I haven't found any better solution yet for this.
So basically on the layout options panel you can select which categories you want to exclude from the filter dropdown panel. So for example if you exclude “category 1”, then posts from category 1 can still be in the results list, however the “category 1” will not be visible in the filter dropdown list.
If you exlclude “category 1” on the advanced options panel, then posts from “category 1” will be excluded – unless they are part of other categories as well. So if a post is part of the “category 1” and “category 2” as well, then it will show up unless you have both categories excluded on the advanced options panel.
This may sound a bit complicated, but unfortunately I see no better way of doing this to fit everybody's needs.
I hope this version will work on your side as well.Best,
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