Thank you for the very detailed feedback and I'm glad you enjoyed it!
The colored keys work by exposing the standard key to extremely high/low temperature for a while, and keep their "form" for half a minute. It's a direct reference to the original Metal Gear Solid where you needed 3 keys to deactivate a nuke, but in the end it was just the same key exposed to different temperatures. I agree that if you don't know the reference it can be a bit obscure to find out, I definitely should have made it clearer.