Non-axisymmetric control coils and the so-called snowflake divertor configuration are two potential solutions proposed to solve two separate outstanding issues on the path towards self-sustained burning plasma operations, namely the transient energy bursts caused by edge localized modes and the steady state heat exhaust problem. In a reactor, these two proposed solutions would have to operate simultaneously and it is, therefore, important to investigate their compatibility and to identify possible conflicts that could prevent them from operating simultaneously. In this work, single- and two-fluid resistive magnetohydrodynamic calculations are used to investigate the effect of externally applied magnetic perturbations on the snowflake divertor configuration. The calculations are based on simulated NSTX-U plasmas and the results show that additional and longer magnetic lobes are created in the null-point region of the snowflake configuration, compared to those in the conventional single-null. The intersection of these longer and additional lobes with the divertor plates are expected to cause more striations in the particle and heat flux target profiles. In addition, the results indicate that the size of the magnetic lobes, in both single-null and snowflake configurations, are more sensitive to resonant magnetic perturbations than to non-resonant magnetic perturbations. The results also suggest that lower values of current in non-axisymmetric control coils would be required to suppress edge localized modes in plasmas with the snowflake configuration.