The absence of Version Control and Base theme in the info.yml file can lead to issues with tracking changes and establishing a foundational theme for the website. This oversight may result in difficulty in managing and coordinating different versions of the code, as well as potential inconsistency in the theme used as the basis for the website. It is crucial to include Version Control and Base theme in the info.yml file to ensure effective tracking of code changes and to provide a cohesive theme foundation for the website.