For new domains you create, you can have Virtualmin automatically generate alias domains like this by going into System Settings -> Server Templates -> Default -> Virtual Server Creation -> Automatically create alias domain.
For example: mydomain.com would create mydomain.com.otherdomain.com
That works pretty well. If you now create a subserver as well, then Virtualmin creates two folders in the domains folder:
subserver.mydomain.com
and
subserver.mydomain.com.otherdomain.com
Why would virtualmin create two folders? This looks like a bug?