3D digital twin layout planning and optimisation can help manufacturers to improve production efficiency and flexibility. Our multi-functional design space integrates closely robot path planning, control synthesis, design validation and metrology simulation, bringing together process-level and system-level objectives. Unlike the traditional design process, 3D digital twin allows us to simulate production scenarios and estimate KPIs, allowing early error detection and a shortened development cycle. These KPIs can guide machine learning models and optimisation algorithms to find the most suitable layout plan. Combining shopfloor data and advanced analytics, our approach supports data-driven decision making for resource allocation and process planning.