Can not define media upload path/URL in multisite

[xtraxtra]

We have a multisite installation with five subdomains. We do not wish to use the default /files/yyyy/mm/filename.ext structure for uploaded media.

In Network Admin > Sites > Edit (under a subdomain) > Settings, you can set:
Upload Path (eg /var/www/pathonserver)
Upload Url Path (eg ​http://www.domain.com/pathonserver)
Fileupload Url (eg ​http://www.domain.com/pathonserver)

However WordPress does not recognise these settings and uses the default format.

If you comment out the last line on wp-includes/ms-settings.php (ie ms_upload_constants()), it does recognise the settings.