https://www.virtualmin.com/node/6087
See if you can enable separate conf files [per Joe] by clicking through:
Webmin | Servers | Apache Webserver | Module Config (at top of page on left side depending on your theme).
You should then be in Virtualmin’s Configurable Options for managing Apache (NOT Configure Apache Modules) and you’ll see several preferences for combined vs separate conf files!
I’m not sure what will happen if you switch after you’ve already created a number of virtual servers. Good luck!