Simulation based Exploratory Learning Environments have a lot of valuable applications in science education especially if it is supported by flexible and robust vitalization tools. Students find it difficult to understand the implications of the Cosmological Principle because they require a higher level of spatial thinking, reasoning and imagination. The paper discusses how visualization tools can be used to explore and study the Large Scale Structure (LSS) of the Universe as a potential method to confront learners' astronomical misconceptions. The evaluation examines whether or not learners' misunderstandings and misconceptions can be rectified through comparative investigations of relevant pre-simulated universes through visual exploration. Depending on the nature of learners' misconceptions, the confrontation process may take various forms such as comparison of LSS growth and evolution and drawing contradictory arguments from simulated cosmological models.