New multisite server: should I use CPanel? And Symlinks?
From the information you've provided, it sounds like CPanel would not be a good setup for you. CPanel is great if you want an easy way to manage separate accounts that don't have access to each other. That's why many resellers use CPanel. You will likely spend just as much time getting around CPanel to do what you want. 

However, keep in mind that CPanel offers a lot out of the box, like email, easy SSL Cert management, DNS management, and monitoring, not to mention security and software updates. If you spin up your own environment, you will need to make sure you set up a firewall of some sort, and an email server, at the very least. Server setup can be a large topic, and is very dependent on your particular hosting needs.

You didn't mention it, but have you looked at Aegir? It may provide you with the multi-site management and update management that you're looking for: http://www.aegirproject.org/

Regarding your proposed directory structure, I have not tested a setup like that so I can't provide a direct answer to your question, but I would look into using Drush and aliases if you haven't already.