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The primary reason you will often find a directory structure like that is that the web host may be storing other types of files for the site that they want associated with the site, but not shared publicly. For instance, on some web hosts you will have a log directory where the logs for just your domain are stored. This way the webhost can give FTP access to the /var/www/html/site1/ directory to the end user and they can access all files related to their service.
One of the original reasons that this directory structure became common is that back in the 90’s when the primary coding language for websites was Perl/CGI scripts, it was common practice to keep these files in a cgi-bin directory outside the main web root rather than having executables within the web root. This is no longer a concern today but the convention lives on.