You can disable this option 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)
In WHM there is "Restrict document roots " setting. If you have enable that option then you can able to create addon domains and subdomains outside of a cPanel user's primary domain's
WHM >> Home >> Server Configuration >> Tweak Settings