There was a new feature added in cPanel 58, that appears to be very handy. This feature allows you to set the default location of addon domains to the main domains home directory, instead of in the main domains public_html folder.
While this doesn’t seem that big, it is very handy. it will help keep .htaccess files from interfering with each other, as well, it will make things more secure, as you now can’t access the addon domains directory from the main domain by simply going to http://maindomain.com/addondomainfolder
To enable this feature, login to your WHM. Click on Tweak settings, then click on the domains tab, and search for, or scroll down to “Restrict document roots to public_html”
Setting this option to “On” means that the document root will be forced to be a sub folder in the public_html
Setting this option to “Off” means that the document root can be in the home directory instead.