One example of this is the innodb_log_file_size
configuration option. As discussed here, there are a series of steps that starts an hour before shutdown and goes to after shutting down. However, this doesn't appear to be documented in the MySQL documentation for this variable and I don't see a list of variables that you may not be able to adjust by simply editing the configuration file and restarting the server.
Does such a list of variables exist? What variables do I need to potentially watch when tuning MySQL to ensure compatibility with existing binary backups?