People shouldn't be putting two things on the buttons that control movement or the gamepad "in-game", and even if they do for things like "save game" or other options, they definately wouldn't use two buttons in place of the NES A button. If the emu looks for just the values contained in the "A Button", "B Button", "Select Button" and "Start Button" for the NES this shouldn't be much of a problem.
And about the color, yeah that's kind of a bummer that we can't use the color if we're pulling this info from the config, but I think that being accurate is more important than asthetics in this case.