We study nonadiabatic coupling in systems of weakly interacting open-shell molecules which have nearly degenerate electronic states and hence significant nuclear derivative couplings. By comparison to numerically calculated nuclear derivatives of adiabatic electronic wave functions, we show that nonadiabatic couplings are represented accurately by diabatization using a recent multiple-propertybased algorithm [T. Karman et al., J. Chem. Phys. 144, 121101 (2016)]. Accurate treatment of weakly interacting molecules furthermore requires counterpoise corrections for the basis-set superposition error. However, the generalization of the counterpoise procedure to open-shell systems is ambiguous. Various generalized counterpoise schemes that have been proposed previously are shown to be related through different choices for diabatization of the monomer wave functions. We compare these generalized counterpoise schemes and show that only two approaches accurately describe long-range interactions. In addition, we propose an approximate diabatization algorithm based on the asymptotic long-range interaction. This approach is appealingly simple to implement as it yields analytical expressions for the transformation to the diabatic representation. Finally, we investigate the effects of diabatizing intermolecular potentials on the nuclear dynamics by performing quantum scattering calculations for NO(X 2 Π)-H 2. We show that cross sections for pure rotational transitions are insensitive to diabatization. For spin-orbit inelastic transitions, asymptotic diabatization and multiple-propertybased diabatization are in qualitative agreement, but the quantitative differences may be observable experimentally.