Thanks - I think I understand your situation now.

Given that systemd doesn't need the PIDFile in this case, I think I
favour removing it from the service file. Users who want to monitor for
a pidfile rather than the systemd service could edit my.cnf as you have
done.

It is a one line change, but might introduce other regressions, so I'm
reluctant to make this change now in Focal unless it is bundled with
some other necessary change, given that as far as I understand it won't
make any difference to users whether this change lands in Focal or not.
It's a bunch of work to prepare, test and land an update. Either way
you'd still need to edit my.cnf for your use case.

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https://bugs.launchpad.net/bugs/1872195

Title:
  PIDFile specified in systemd unit file but pid-file not in my.cnf

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