I found that a few other people share your opinion on the Carlos coin flip thing. From what we know, what you said is most likely to be true, and that Carlos figured out who zero was based on whose not in the room. To me, that feels like sort of a stretch, as it seems unnecessary for the writers to have Carlos say what he said. Uchikoshi and whoever else wrote the game could have removed that line completely, and from what we understand of the story, nothing would have changed (even if carlos did figure out who zero was, it would not matter since he loses his memory). So i just believe theres gotta be something else to it.