This is a side-effect of the application not having a table prefix or suffix feature. Some applications need to have their own database (e.g. with no other applications sharing it). It’s often wise to give apps their own database, regardless. In some cases, you need them in the same db (some Joomla bridged applications need to share a database for authentication and synchronization purposes, for example), but if they aren’t going to be working together, give them their own db.
Don’t do it by hand! Of course it’s a task for Virtualmin.
I’m saying, allow your virtual servers to have more than one MySQL database, and Virtualmin will offer to create a new one when you use Install Scripts.