I actually did notice the same last time I set up a new server, this happened on both Ubuntu and Debian at least.
The work-around is in the terminal to;
virtualmin modify-web --no-webmail --domain yourdomain.tld && virtualmin modify-web --webmail --domain yourdomain.tld
The weird part is that the Apache config for said domain looks very similar before and after the change, but I didn’t have time to go through the details enough so I could file a bug-report with the Virtualmin staff yet.