I know that I can put the files of add on domains into subdirectories of public_html. But I don’t like that this means I can see a subdomain’s files from the main domain as a folder.
For example, if my main account domain is “prime.com” then “public_html” holds all the prime.com files. I may have an add on domain “second.com” in the folder “public_html/second” but then I can also reach these files via “http://prime.com/second”. I would like to put the files for prime.com into “public_html/prime” instead.