There's an option to disable this here:
WebHost Manager »Server Configuration »Tweak Settings, Domains tab:
Restrict document roots to public_html [?]
Enabling this setting restricts Addon and Sub Domain document root directories to the same document root as an account’s primary domain (~/public_html)
Enabling this setting restricts Addon and Sub Domain document root directories to the same document root as an account’s primary domain (~/public_html)
