Is it permissible for a worshipper to pray with an Imam who habitually combines prayers with the intention of it being a supererogatory prayer, and then to pray it again with the intention of it being an obligatory prayer at its prescribed time, and does this contradict the Imam's intention?

The prayer of one performing a supererogatory prayer behind one performing an obligatory prayer is valid, according to the preponderant opinion. Your prayer behind the imam is valid with the intention of performing a supererogatory prayer. If the imam's prayer is not valid as an obligatory prayer due to the invalidity of combining prayers, it then becomes a supererogatory prayer. In this case, your prayer behind him is valid, as it is a supererogatory prayer behind another supererogatory prayer.