Elaborating from previous answers (which do not still convince me) I've come to this. I'll not accept it automatically, I want to see what do you think about it.
Colours would be something like security contexts. You belong to the blue security set (user programs), to the red security set (MCP programs), to the purple security set (guest programs).
Flynn was able to switch from one security context to another (this is supossedly impossible to do for a program, but well, he is not a program) and get the "permissions" of an MCP program in front of the Operating System.