There are too many things that could go wrong for users if the server itself 
ignores something in the config file and uses what it considers a safe default.

For the packaging we are working on working around the issue of the
server not starting in cases where users have disabled the automatic
starting/stopping of services, and this could potentially be extended to
include cases where the config contains invalid options (i.e. print a
warning and don't try to run mysql_upgrade instead of throwing an

But this might not cover all the use cases you mention, since some of
those packages might be expecting the server to be up and running.

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  mysql fails to start after upgrade if previous defaults were

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