Recent research has highlighted the limitations of relying solely on physical building components for integrating architecture engineering and construction (AEC) disciplines. While construction management can benefit from such models, they do not formalise spatial configuration that is crucial throughout a building’s lifecycle. This paper explores the often-overlooked role of spatial topology in digital building models, emphasizing its importance in architectural design on one side and the technical development on the other side. Conventional BIM software primarily focuses on physical elements like walls, roofs, and columns, neglecting the spaces they enclose. This approach, while effective for representing tangible building components, fails to capture the comprehensive representation of space. The lack of spatial relationships and dependencies in these models can significantly impact the planning and execution of various architectural as well as engineering tasks as well as digital comprehension and automation fore and beyond construction. The research is stemmed from observations and studies of challenges in sustainable modular prefabrication of housing. Modular fabrication faces difficulties in producing adverse reliable proposals and maintaining economic resilience amidst market demand fluctuations. Three main obstacles have been identified in developing resilient configurable building systems: This study underscores the need to consider spatial functional configuration and adaptability from the conception and moving beyond the current limitation of physical building elements in AEC integration. By addressing these challenges, from ground up the industry could develop more flexible, sustainable, and resilient building systems that better respond to market demands and technological advancements throughout the building’s lifecycle.