More technically, those documents (and other Apple-spawned formats such as TextEdit's .rtfd) are "document bundles"—a directory hierarchy with a file extension or xattr that makes Launch Services treat it as a file. (The most well-known document bundles being macOS applications.)
The storage frameworks used for accessing the contents of document bundles treat zip archives as transparent, so a document bundle is still a document bundle if you zip its contents and then give it the name of the original directory.
And the reverse is also true: take, for example, an .epub (which is a zipped hierarchy of HTML files) and unzip its contents into a new directory. Name that directory "foo.epub". iBooks will happily open this "file." And it stores the .epubs you've imported into your iCloud Library this way on disk!
The storage frameworks used for accessing the contents of document bundles treat zip archives as transparent, so a document bundle is still a document bundle if you zip its contents and then give it the name of the original directory.
And the reverse is also true: take, for example, an .epub (which is a zipped hierarchy of HTML files) and unzip its contents into a new directory. Name that directory "foo.epub". iBooks will happily open this "file." And it stores the .epubs you've imported into your iCloud Library this way on disk!