root user question

I do a little of both. I've never memorised the root password for Virtualmin.com (I use an ssh key when I need to login as root), so I created a joeroot user that uses my regular virtualmin.com password, but it has all the privileges of root. But on most of our systems, I just use root.

It doesn't really matter, and there are lots of authentication options, so the Webmin and system root passwords don't even need to be the same (but if you have either, you can reset the other--root on the command line and root in Webmin are equally powerful).

No real pros or cons that I can think of, as long as you've got encryption enabled in Webmin. Just remember that a root level account in Webmin/Virtualmin is all-powerful, and so if you're using it from an Internet cafe or something, you'll want to proceed with caution (probably shouldn't do that at all, actually, since even if you clear history when you're finished, a key sniffer would still get your password).