The BNS/cookedpc folder is for the general kinda stuff like clothings what not, so basically like the whole game without localization.
For example the english voice over, since the english/cookedpc folder is for localization, those jp voice will conflict with the english voice, you have to either overwrite them, which the launcher will download the english VO again or you use launcher bypass to ignore the file checks, otherwise you will have to deal with the pop ups. The only reason there is pop up when you launch the game is because english/cookedpc folder has another item with the same name.