The development of digital twins in the built environment projects facilitates decision making during both the planning and execution phases, while also contributing to the digitalization of the built environment. Open standards models such as Industry Foundation Classes (IFC) and CityGML representing Building Information Modelling (BIM) and Geographic Information Systems (GIS) are essential components in the creation of a comprehensive digital twins. Accurate georeferencing of these models is critical for performing reliable geospatial analysis, including distance and area measurements. This factor has major effect on projects that employ a custom Coordinate Reference System (CRS), or in contexts where the distortion due to map projection is significant. Although a considerable number of studies addressed georeferencing in BIM-GIS data integration, limited has been given to the assignment of custom CRS to both IFC and CityGML models. Additionally, the effect of modelling and georeferencing methodologies on the final positional accuracy of the models remain insufficiently explored, and most of existing studies remain at the conceptual level. This study aims to address this gap by proposing a methodology to assign custom CRS to both IFC and CityGML models, while also practically examining how BIM modelling and georeferencing methodology impact the overall georeferencing accuracy of the models. The results demonstrate the effectiveness of the proposed approach in controlling the georeferencing accuracy of IFC and CityGML models employed in the generation of digital twins. The proposed approach can be utilized as a guideline for achieving accurate georeferencing when creating digital twins in the built environment projects.