I don't want this to show up.
The only option for this I found is this one and it is already unchecked:
Copy whenexists=merge will stop it happening in the case of copying a folder out of an archive (possibly except zips, which may be handled differently).
I'm not sure why the Preferences setting isn't doing the same thing here. I've made a note to look into it.
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Thank you, but this one still shows up with Copy whenexists=merge
Out of a zip though, yeah. How could I solve that there? Not needing to extract zips first before working with their content is kinda a key feature for me.
I don't think it can be suppressed for zips, if the target folders already exist.
Why not? 
You mean currently, or at all?
It's definitly something that would be nice. I need that often for mods, which come in archives and contain the same folder structure as the game folder and they always have to be merged.
Like this:
It even asks when I do Copy Force 