[Mashiro]

You're not bound to use any kind of defaults that come with software. /var/www is such a default that is commonly used by web servers as their default web root. However you can create yourself a folder somewhere and use that as your web root given you setup the permission correctly. You can use different web roots per vHost / each webpage. That is exactly what panels do. They use custom path for every user and their websites. Infact I did so with Nginx already in the past. Every website has had its own web root with sub folders for the website files, logs, certificates and etc. I made the vHost process for that website run under its own user and even created a dedicated PHP-FPM instance running under the same user just for that vHost. It's not that much work once you get it working and documented once. Panels do the same - they use preconfigured templates where just a few things corresponding to the website/user you create are changed. So behind a few clicks is a chain of commands and files that you would manually create when working without the panel.

Panels however are blackboxes. They might do things a lot different than you might do it. You however won't know how exactly everything is done without having to look at a lot of the source code and files. Moreover panels add another layer of security risk.