If you select an associated file, a copy will be sent to the same directory as the original file.
This will always work but Composer also adjusts the links in the main file to point to the items included in this way. So the published file is not identical to the original. It is also tied to the other items in that same directory.
The disadvantage is that if you send the same file to two different directories, two different copies of associated files will be sent.