Multisite and Domain mapping media upload issue

These are systems I’ve inherited so I cannot answer how it worked before domain mapping was enabled, but from the nature of our sites it *should* have always been there.

We do have some sites that are mapped to subdomains.
So aaa.domain.com is mapped to blah.aaa.com. To stop the domain mapping plugin from adding the www we edit the domain mapping plugin as show below. That is also the only place I see a redirect adding a www in either the .htaccess, apache vhosts, W3TC, domain mapping etc. For those sites we :

domain_mapping.php
starting at line 511

$wpdb->suppress_errors( $s );
$protocol = ( 'on' == strtolower( $_SERVER['HTTPS' ] ) ) ? 'https://' : 'http://';
if ( $domain ) {
    if( $domain == 'blah.aaa.com' ||
        $domain == 'blah.bbb.com' ){
            $return_url[ $wpdb->blogid ] = untrailingslashit( $protocol.$domain );
    } else {
        $return_url[ $wpdb->blogid ] = untrailingslashit( $protocol.'www.'.$domain  );
    }

.htaccess
———

# BEGIN W3TC Browser Cache
<IfModule mod_deflate.c>
    <IfModule mod_setenvif.c>
        BrowserMatch ^Mozilla/4 gzip-only-text/html
        BrowserMatch ^Mozilla/4\.0[678] no-gzip
        BrowserMatch \bMSIE !no-gzip !gzip-only-text/html
        BrowserMatch \bMSI[E] !no-gzip !gzip-only-text/html
    </IfModule>
    <IfModule mod_headers.c>
        Header append Vary User-Agent env=!dont-vary
    </IfModule>
    AddOutputFilterByType DEFLATE text/css application/x-javascript text/html text/richtext image/svg+xml text/plain text/xsd text/xsl text/xml image/x-icon
</IfModule>
<FilesMatch "\.(css|js)$">
    FileETag None
    <IfModule mod_headers.c>
         Header set X-Powered-By "W3 Total Cache/0.9.1"
    </IfModule>
</FilesMatch>
<FilesMatch "\.(html|htm|rtf|rtx|svg|svgz|txt|xsd|xsl|xml)$">
    FileETag None
    <IfModule mod_headers.c>
         Header set X-Powered-By "W3 Total Cache/0.9.1"
    </IfModule>
</FilesMatch>
<FilesMatch "\.(asf|asx|wax|wmv|wmx|avi|bmp|class|divx|doc|docx|exe|gif|gz|gzip|ico|jpg|jpeg|jpe|mdb|mid|midi|mov|qt|mp3|m4a|mp4|m4v|mpeg|mpg|mpe|mpp|odb|odc|odf|odg|odp|ods|odt|ogg|pdf|png|pot|pps|ppt|pptx|ra|ram|swf|tar|tif|tiff|wav|wma|wri|xla|xls|xlsx|xlt|xlw|zip)$">
    FileETag None
    <IfModule mod_headers.c>
         Header set X-Powered-By "W3 Total Cache/0.9.1"
    </IfModule>
</FilesMatch>
# END W3TC Browser Cache

RewriteEngine On
RewriteBase /

#uploaded files
RewriteRule ^(.*/)?files/$ index.php [L]
RewriteCond %{REQUEST_URI} !.*wp-content/plugins.*
RewriteRule ^(.*/)?files/(.*) wp-includes/ms-files.php?file=$2 [L]

# add a trailing slash to /wp-admin
RewriteCond %{REQUEST_URI} ^.*/wp-admin$
RewriteRule ^(.+)$ $1/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule . - [L]
RewriteRule  ^([_0-9a-zA-Z-]+/)?(wp-.*) $2 [L]
RewriteRule  ^([_0-9a-zA-Z-]+/)?(.*\.php)$ $2 [L]
RewriteRule . index.php [L]