Machine login for Microsoft SQL Server for Linux
I checked in with the WHM+cPanel - the company behind the hosting control panel and they said they store their MySql root user password on a local file on disk as well for doing all the automated maintenance, creation etc. 

Excerpt from their docs: 
By default, cPanel &amp; WHM's implementation of MySQL stores the MySQL root account password in the /root/.my.cnf configuration file. Do not edit this file manually. 

I'm going to end up with doing the same, and storing the file (read only) in the same /root/ folder.