A clean magnetic boundary, i.e. a vanishing radial magnetic field, is important for reversed field pinch operation. In order to achieve this target a large modification of the RFX device (a = 0.45 m, R = 2 m) into RFX-mod has been realized and 192 individually controlled saddle coils which provide a flexible control of magnetic boundary have been installed. Recent experiments have shown that this change has produced a significant improvement in plasma magnetohydrodynamic (MHD) behaviour.This paper discusses 3D MHD numerical simulations aimed at interpreting these results. In particular it is shown that these simulations can predict the measured level of magnetic fluctuations in different operational scenarios. They can also predict the dominat modes and show in general an agreement with experiments. A specific comparison for a resistive wall mode branch is also done, showing differences between simulations and experiments which may indicate the presence of field errors.