When mediawiki is configured and running from the top directory of the web server using the following variables:
$wgServer = "http://www.example.com"; # whatever the real site name is
$wgScriptPath = ""; # empty for serving the wiki from / on the server
Where wgScriptPath is empty and all scripts are in the root directory of the server, base_url does not get set in Collection.body.php when being set via wfExpandUrl( $wgScriptPath, PROTO_CURRENT ). Simply moving all the wiki files into one directory deeper and setting wgScriptPath to the new directory confirms this behavior.