That seems to be a question you should be asking your server host. I would have no way to answer a question on why your web server operates the way it does. That is solely a server question on its operation and has nothing to do with our specific application.
I would assume that cpanel restores directories and files based off the default server setup on what a directory and file permission are for that specific setup. By default with most servers a directory is 777 and file 644. I would assume your backups just restore stuff based on the default server setups and not to permissions you might have applied to specific files and directories.
Your host would be able though to assist in an explanation of how there server operates.