Exactly, that's why Tobi/ Obito was able to convince him that he was Madara, because Kisame only heard things about Madara and never actually met him.
Once Tobi /Obito convinced him he was Madara, Kisame always connected Obito's face with Madara, hence why he identified Obito as Madara in chapter 404.
I don't exactly see what you are trying to get at or what you think is a plot hole...
But that doesn't explain this:
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Kisame sees the sharingan, then he asks him who he is, knowing it must be a skilled uchiha, of course, but he doesn't believe him when he says he is Madara, he thinks Madara is dead, so he wants him to step out of the dark, but seeing how he looks would prove nothing. Of course we don't see more of what happens, but I just can't see that Tobi/Obito could possebly prove it to him. Maybe he just accepted it and had his doubts, but later when he sees him again he seems sure, or maybe he doesn't really believe, but he has no reason to question it, as he said, he lives in a world full of lies.