Madhura,
in https://sourceforge.net/p/phpmyadmin/bugs/4676/ issue 3, I was not against creating these tables automatically; I was against creating them without notifying the user.  Also, I believe that PMA_checkAndFixPMATablesInCurrentDb() has two purposes: creating the tables if they don't exist, and setting the correct globals if they exist, so that the rest of the logic use them.