We report on the implementation of a versatile projection-operator diabatization approach to calculate electronic coupling integrals in layered periodic systems. The approach is applied to model charge transport across the saturated organic spacers in two-dimensional (2D) lead halide perovskites. The calculations yield out-of-plane charge transfer rates that decay exponentially with the increasing length of the alkyl chain, range from a few nanoseconds to milliseconds, and are supportive of a hopping mechanism. Most importantly, we show that the charge carriers strongly couple to distortions of the Pb-I framework and that accounting for the associated nonlocal dynamic disorder increases the thermally averaged interlayer rates by a few orders of magnitude compared to the frozen-ion 0 K-optimized structure. Our formalism provides the first comprehensive insight into the role of the organic spacer cation on vertical transport in 2D lead halide perovskites and can be readily extended to functional π-conjugated spacers, where we expect the improved energy alignment with the inorganic layout to speed up the charge transfer between the semiconducting layers.