I just had this sweet idea and figured what better place to discuss it than on the Virtualmin forums!
My idea is to add a new option to choose the port when creating a new virtual server within Virtualmin.
When creating the new server an option can be added to specify the port that the webserver runs the site off of, including if it is a SSL site or not. Furthermore this would allow you to use one single SSL certificate for multiple sites installed along the same domain, instead of using subdomains.
However the issue is that you would have to be able to use the same domain name but have multiple different sites on different ports. i.e. example.com:444, or example.com:1234.
Maybe you could use folders with ports like /home/username/ports/444/public_html/ and make the ports folder configurable somehow.