How can I set specific download URI for file?
The proper solution is a hook_menu, which I believe is also going to be a requirement to make this reasonable when several sites want separate names.

I workaround would be to just symlink it to your Drupal root.

ln -s sites/example.com/files/somefile.xml some.xml


But if it's a requirement to have each filename only available on one domain, apache would need to have logic to block the "wrong" names, which is inconvenient.

A third possibility would be to rewrite the URL in apache, but I don't exactly know the syntax for this.