We dont really know that. It all depends on the tone of voice he used when saying "as the Penguin". I mean, he obviously knew what role they meant Phillipe for, but perhaps he hadn't heard of Hoffman as Penguin so he was just surprised about that.
Some of you people are looking into his exact wording too much. this isn't one of his movies, just an interview. There's no hidden meanings to the way he said it.
Besides, this would be like asking Nolan "Why did you decide to cast Heath Ledger?" and him replying "No, Heath Ledger's not in the Prestige!"