Conventional Molecular Dynamics (MD) models of bitumen are built by homogeneously mixing molecules in a volume without considering that the molecules in bitumen are known to exhibit phase behavior and form distinctive molecular arrangements. These are known to have a significant impact in the behavior of bitumen, and considering their existence is paramount in producing improved representations of bitumen using computational models. This study explores whether MD models of bitumen that are conventionally assumed to be in equilibrium can still undergo significant phase separation over considerably long simulation times. It also aims to establish a more formal pathway to build and study models with highly heterogeneous arrangements of their molecules. Moreover, it aims to evaluate whether the presence of distinct morphologies have a significant impact in numerous physical properties of bitumen. The study shows that conventional and widely used models of bitumen exhibit significant molecular rearrangements over long times (>360 ns). It also shows that building heterogeneous morphologies is possible and result in energetically favorable conformations. Moreover, it proves that studying properties regularly used to validate MD models of bitumen (e.g., density) are insufficient in assessing the impact of different morphologies; more thorough methods are required to evaluate them.