The concept of digital twins holds significance in streamlining the design, testing and optimisation. In this work, we use surrogate models as digital twins to model the EMC of buck-boost converters which are widely used in automotive industries. EMC has become important consideration because of increasing electronic systems and their miniaturization. Common mode (CM) emissions increase in the case of buck-boost converters because of their higher switching of SiC/GaN transistors. Hence Electromagnetic Interference (EMI) filters are used with these converters to comply with EMC limits. However, designing such a system becomes quite intricate when many key performance indicators (KPIs) are involved as well as conflicting in nature. In addition, objectives like cost and volume must be considered. Such a system requires MOO which becomes a tedious task with full 3D simulations as it can lead to large simulation times. With surrogate models as digital twins, we can have a virtual representation of the EMC of such a system that allows us to compute 10000 evaluations in 4-5 minutes which eases the burden of MOO. By considering all the design parameters that concern both the functional and EMI design of the system, we build surrogate models and use MOO on top to find better tradeoffs between the KPIs to obtain Pareto-optimal solutions.