If the option “movies are in a seperate folders…” is enabled Kodi will look to the name of the folder containing the movie for matching media info, and otherwise use the name of the file itself, simple as. This is just a matter of the users preferences on how they structured their files. Kodi couldn’t care less if you use subfolders or not. I’m not aware of any benefit to a flat file structure as during scans it will skip folders that haven’t changed the same as it skips files in a source root that haven’t changed. My personal preference is to keep each movie in its own subfolder so I don’t have as many items in the root (ie just a folder for “movie” instead of movie.mkv, movie.en.srt, movie.jpg, etc) but I’ve not seen real world where there was any particular advantage with scraping in Kodi deciding to use one style over the other.