© 2017 American Physical Society. Commensurability oscillations in the magnetotransport of periodically patterned systems, emerging from the interplay of cyclotron orbit and pattern periodicity, are a benchmark of mesoscopic physics in electron gas systems. Exploiting similar effects in two-dimensional materials would allow exceptional control of electron behavior, but it is hindered by the requirement to maintain ballistic transport over large length scales. Recent experiments have overcome this obstacle and observed distinct magnetoresistance commensurability peaks for perforated graphene sheets (antidot lattices). Interpreting the exact mechanisms behind these peaks is of key importance, particularly in graphene, where a range of regimes are accessible by varying the electron density. In this work, a fully atomistic, device-based simulation of magnetoresistance experiments allows us to analyze both the resistance peaks and the current flow at commensurability conditions. Magnetoresistance spectra are found in excellent agreement with experiment, but we show that a semiclassical analysis, in terms of simple skipping or pinned orbits, is insufficient to fully describe the corresponding electron trajectories. Instead, a generalized mechanism in terms of states bound to individual antidots, or to groups of antidots, is required. Commensurability features are shown to arise when scattering between such states is enhanced. The emergence and suppression of commensurability peaks is explored for different antidot sizes, magnetic field strengths, and electron densities. The insights gained from our study will guide the design and optimization of future experiments with nanostructured graphene.