OK, you are right, he is using "color" in a funny way to reflect the idea that the violation is somehow in those bits. But in my opinion, the violation is in the channel as a whole (the ciphertext, the one-time pad, and the instructions on how to decrypt, shared for the purpose of distributing copies), not because of "colored bits".
Your opinion is an engineer or computer science opinion. I am not criticizing when I say that; I share it with you. But the opinion of most of the rest world is not with us, and this is a good essay explaining that opinion. It is important to understand it if you want to understand the world, make correct predictions about how most people will operate in these matters, or figure out how to best change people's minds. (I can definitely speak from experience that the direct approach is not very effective. Can't tell you what is, unfortunately...)
No, the author would say the opposite. That’s the whole point - the process by which you get to the bits matters.