This is a new Virtualmin installation and I was able to reproduce the bug again after another fresh install. It seems to be a new bug, since I’ve been using Virtualmin with Nginx without issues, and this is the first time I’ve seen this issue with disabling Apache.
The reliable way to install Ngnix and its Webmin modules is to start out that way with the Virtualmin install script on a clean server. Read this or type ./install.sh --help in your terminal for all options.
I’m not sure re-running the script with --bundle LEMP will help with your problem unless it’s a fresh install on a clean server with no traces of Apache. Before trying the script a second time you might try removing Apache entirely making sure all its *.conf files, modules and .htaccess files are absent. On the other hand, if it’s a new server you have the luxury of starting over.