Comment 1 for bug 1072695

This was fixed in the linked branch by changing innobackupex so that $backup_dir/backup-my.cnf is always used on --apply-log (even if there's a defaults file specified on the command line).

I don't think there's much use in overriding backup-my.cnf on prepare. In rare cases when someone somewhere may want to do so, one can always replace or edit backup-my.cnf to override some parameters.