addon domain is a separate domain point to additional websites, it can be under /main_root/addon_domain_folder/ or it can be under /main_root/publich_html/addon_domain_folder, it has no link to primary domain, and search engine will treat them separately.
However, unlike primary, it doesn't have its own cPanel, it still can create email account, redirects, install and subdomains, but for ftp acc, the username will be username@primary_domain.com and ftp server still shows as primary_domain.com. Thus other than ftp acc, it is able to show no connection to primary domain
If you make sure no url link from primary domain to addon domain, the search engines won't find them through primary domain. such as primary_domain.com/addon_domain_folder, or addon_domain_subname.primary_domain.com. Thus it is better to put folder structure as primary domain web sits at /main_root/publich_html, addon domain web sits at /main_root/addon_domain_folder