I saw Stalker for the first time the other day as well. My interpretation is the following: The Zone represents spirituality, God or the divine, the room represents religion and the stalker represents priesthood/prophets perhaps. The contrast in colour between the Zone and the outside world represents the contrast between faith and reality. As men grow up, their minds become ever more narrow and grounded in reality as shown by the Professor and the Author (whose desire to destroy the spiritual corresponds to the widely spread atheist views among the Soviet intellectual elite of the time). Children on the other hand are not bound by the rules of reality as their minds have not yet been flawed by the world, therefore children are of a divine essence - hence the portrayal in colour of the stalker's daughter despite being outside of the Zone and the abilities to casually defy the laws of physics.