The Physikalisch-Technische Bundesanstalt has developed a reference setup for measuring the modulation transfer function (MTF) of camera lenses with the goal of reaching an expanded measurement uncertainty of 0.01 (coverage probability of 95%) for various measurement configurations. We present optomechanical simulations of the setup behavior, which are used to investigate the influence of the combined mechanical misalignments on the MTF depending on the lens under test. The investigations are carried out as part of Monte Carlo studies for different sample lenses and field heights considering the correlations between the effects of different positioning errors on the MTF measured. The results of the sensitivity analyses have allowed appropriate alignment strategies to be identified that significantly reduce the uncertainty contribution of the positioning errors. By implementing these strategies, the target measurement uncertainty can be achieved for most of the desired measurement configurations. In addition, the comparison of three different sample lenses shows that the MTF sensitivity to misalignments strongly depends on the characteristics of the lens to be measured.