I honestly cant understand why I must have a lot of extra work to clean out the extra subdomain admin and webmail from the virtual server config file before I request certificates. If I want them as subdomains I create them, now they are just annoying. What is the reason behind?
I always install VIrtualmin using the minimal flag and if required, manually set up any (mostly mail-related) modules after so the only subdomain created is www.
Also, that means you almost certainly have features enabled that you aren’t using…spending a little time getting familiar with the configuration options in Virtualmin is worthwhile. (Features and Plugins is where you can disable features, and should be your first stop after installation if you won’t be using all the features.)