mysql.allow_persistent = ?

A php web apps persistence to mysql is determined by the php web apps coding itself. The mysql http://php.net/manual/en/mysql.configuration.php#ini.mysql.allow-persistent and mysqli http://php.net/manual/en/mysqli.configuration.php#ini.mysqli.allow-persistent set *.allow-persistent so be left alone at defaults as it is just a global setting to whether to allow or not allow mysql or mysqli to set and enable persistence when the individual php web app wants to control it (set persistance on or off).

so whether it's better to have persistent connections from php and mysql depends entirely on the php web app in question and your traffic/load patterns.