This is a duplicate of How to change the Document root of the Sub-server which is kind of a duplicate of this Avoide creation of Admin user of subdomain in the virtualmin
They all boil down to you’re trying to do really complicated stuff to avoid changing what is hopefully one line of configuration in your web applications. That’s probably a bad idea.
Virtualmin puts homes in /home. You can force it to put things in /var/www, but you almost certainly would have to do a lot more work to do that than just update your apps.