Regarding Settings -> Preferences -> Folder Tabs -> Options -> File display close button only closes active tab , this description would make me think that if the option is not checked, clicking the close button would close all tabs. What actually happens when the option is not checked is that the close button disappears. This may be what is intended to happen but it doesn't really match the wording.
I'd probably have it close the entire lister which sort of seems to me consistent with closing the entire second file display, but I think it's a very minor matter of personal preference.