despite contract extension clause, player arranges transfer to other club

He isn't staying. The new contract will supersede any untriggered clauses in the old contract. 

If a player can be approached before a contract clause is triggered and they agree a new deal that would invalidate the triggering of the clause. It's unfortunate to lose the player in this situation, but it is correct. 

oh damn, didn't know that.

Thanks for the answer!