Summary
Each Addon Domain requires a subdomain. Using mod_rewrite you can stop people from being able to use the addon domain as a subdomain of the primary domain
Preventing use of the Subdomain
Put this in the .htaccess file located at the subdomains folder, changing the subdomain, primarydomain.com and addondomain.com:
RewriteEngine On
RewriteCond %{HTTP_HOST} ^subdomain.primarydomain.com$ [OR]
RewriteCond %{HTTP_HOST} ^www.subdomain.primarydomain.com$ [OR]
RewriteCond %{HTTP_HOST} ^addondomain.com$
RewriteCond %{REQUEST_URI} ^/$
RewriteRule ^(.*)$ http://www.addondomain.com/ [R=301,L]
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