We present a mathematical derivation of some of the most important physical quantities arising in topological bilayer systems with permutation twist defects as introduced by Barkeshli et al. (Phys Rev B 87:045130_1-23, 2013). A crucial tool is the theory of permutation equivariant modular functors developed by Barmeier et al. (Int Math Res Notices 2010:3067–3100, 2010; Transform Groups 16:287–337, 2011).