Tolerance analysis is crucial in every manufacturing process, such as electrical machine design, because tight tolerances lead to high manufacturing costs. A FEM-based solution of the tolerance analysis of an electrical machine can easily lead to a computationally expensive problem. Many papers have proposed the design of experiments, surrogate-model-based methodologies, to reduce the computational demand of this problem. However, these papers did not focus on the information loss and the limitations of the applied methodologies. Regardless, the absolute value of the calculated tolerance and the numerical error of the applied numerical methods can be in the same order of magnitude. In this paper, the tolerance and the sensitivity of BLDC machines’ cogging torque are analysed using different methodologies. The results show that the manufacturing tolerances can have a significant effect on the calculated parameters, and that the mean value of the calculated cogging torque increases. The design of the experiment-based methodologies significantly reduced the calculation time, and shows that the encapsulated FEM model can be invoked from an external system-level optimization to examine the design from different aspects.