It took me a while to understand what's going on here (I think), but can someone explain to me if there are security risks with regards to my logic of what's going on here as I am trying to set up a home web server as a developer with some good Linux knowledge?

Ubuntu is not like other systems, as it has restricted the root user account. You can not log in as root or su to root. This was a problem for me as I have had to install numerous applications and services to /opt as per user documentation (XAMPPfor Linux is a good example). The problem here is that this directory is owned by root:root. I notice that my admin user account does not belong to root group through the following command:

groups username so my understanding is that even though the files and services that I place in /opt belong to root, executing them by means of sudo (as required) does not mean that they are run as root? I imagine that the sudo command is hidden somewhere under belonging to the root user and has a 775 permission? So the question I have is if running a service like Tomcat, Apcahe, etc exposes my system like on other systems? Obviously I need to secure these in configurations, but isn't the golden rule to never run something as root? What happens if I have multiple services running under same user/group with regards to a compromised server?