Hmmm, as it stands, autoptimize is hardcoded to output aggregated files to the wordpress wp-content-directory, whatever it may be named, relying on wp_content_url (via the function content_url()) and wp_content_dir (both of which are part of WordPress core, they're not AO-specific).
So if you'd want autoptimize to output aggregated files elsewhere (i.e. in our uploads directory), you'd have to make changes to the plugin's code, rather then using API-functions or changes to wp-config.php I'm afraid.
Pretty surprised that changing wp-content_url sitewide impacted your wordpress backend ...
frank