So, I have become very good at checking the MySQL setup, and in my case
(I recently restarted my server) I had AppArmor properly setup but it
still would not work

My previous actions, as pointed out, disabled AppArmor why it after that 
started working
@seth-arnold Seth Arnold pointed out the correct solution in #6

The proper solution is:

       systemctl reload apparmor.service

- which applies the current and extensively checked settings, this apply
which apparently had not been done, and this keeps AppArmor active and
MySQL working

The question might be why are the settings not applied even on a server
reboot?

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https://bugs.launchpad.net/bugs/1610765

Title:
  Apparmor refuses mysqld open on /etc/mysql/my.cnf.migrated causing it
  to fail to start

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