What does it mean for `cp -a` to "not [preserve] directory structure"?
It means that if you copy into an existing directory it will not delete existing files and subdirectories (and existing subdirectories will have their existing permissions and ownership information, even if there is a directory of the same name in the source copy). This is equivalent to the "merge" option when copying a folder in the Finder, and there is no equivalent to the replace option.