We develop transformative Model-Based Systems Engineering (MBSE) methods that establish a traceable digital thread for advanced aircraft propulsion system design. Our work focuses on creating formalized frameworks that link requirements, functions, logic, and physical components within an integrated SysML/MagicDraw environment. By advancing how complex systems are modeled and connected, these methods enhance collaboration across disciplines, reduce integration risks, and enable faster, more transparent evaluation of emerging propulsion technologies and architectures.