FWIW, I have used the add-one-book-per-directory option on an actual calibre library on several occasions. It works just fine.
Generally, we recommend people forget about the library folder simply because most users are prone to doing things they didn't mean to or shouldn't do -- like editing the files, moving folders, etc. -- and expecting calibre to pick up on that.
The metadata.opf records the metadata from the book
record, and when importing with the one-book-per-directory method, any and all formats in that folder will be added with the OPF metadata.
Side note: filenames ending in a dot are valid filenames. Windows doesn't like that because it likes to conceal complexity from the user, and apparently that results in some bugs.

Just like filenames that begin with a dot, which IIRC Windows willtry to stop you from creating, but unix software ported to Windows like Apache webserver require. e.g. the .htaccess file.
The NTFS filesystem allows certain things that Windows doesn't (and IIRC that includes case-sensitivity in filenames. Create it on linux, and it will show and cause errors on Windows). But there are no Windows APIs to do that AFAIK.