He didn't even use any abilities aside from Kamui against Minato. It's not like he was super powerful, he was just able to avoid being hit for a while. Until Minato figured out his ability and kicked his ass.
That has nothing to do with Chakra. He thought that Tobi was Madara, only because Tobi called himself Madara, or at least allowed Minato to assume he could have been Madara.Kurama spoke about Sasuke's chakra being more sinister than his own, like Madara's was. Yet in the case of Tobi he doesn't imply Tobi is like Madara but that he IS Madara.
Actually, come to think of it. Has Kurama ever actually referred to Tobi at all? We know he mentions Madara a few times, but how do we know he isn't talking about the real Madara each time?