You can make modifications to how Virtualmin writes logs in either the GPL or Pro versions – but being able to do so from the command line is a Pro-only feature.
The GPL version generally offers a way to resolve issues like this one Virtual Server at a time. Pro offers a way to do it for lots of Virtual Servers at once
You can enable it in the GPL version by going into System Settings -> Server Templates -> Apache Website – then look for "Write logs via program".
-Eric