This has come up a bunch in recent months/years, and I've even seen it myself on a couple of test installs on virtual machines.
A lot of times, there will be a root password set for MySQL, but the user doesn't know it, and so Virtualmin makes them do a clumsy bouncing around between Webmin (and maybe command line; I don't think even the Webmin module will correctly handle resetting a password if you don't know the original one).
There should be a "go nuclear" sort of option, to allow the user to tell Virtualmin to force a reset of the root password, if they don't know the existing one. This would, of course, need to go through the rigamarole of stopping MySQL, starting it with --skip-grant-tables and --skip-networking options, resetting the password, and then restarting it normally. But, it'd make a lot of customer complaints/confusions go away.
We also probably need a better error message. But, I guess if we just added a checkbox to say "force reset of root password", that'd make it less of a big deal that the error is scary for some.