Setup a new user for PMA:

mysql -e "CREATE USER 'pma'@'localhost' IDENTIFIED BY '';"
mysql -e "GRANT ALL PRIVILEGES ON *.* TO pma@localhost WITH GRANT OPTION;"

To setup a configuration that uses the config file for authentication, and ignores the mysql and information_schema tables, here is what to add to

$cfg['Servers'][$i]['auth_type'] = 'config';
$cfg['Servers'][$i]['user'] = 'pma';
$cfg['Servers'][$i]['password'] = '';
$cfg['Servers'][$i]['hide_db'] = '^(mysql|information_schema|performance_schema)$';
# $cfg['Servers'][$i]['only_db'] = array('');

Disable version check, which runs over http and breaks the https seal:

$cfg['VersionCheck'] = false;