The influence and validity of wall boundary conditions for non-equilibrium fluid flows described by the Boltzmann equation remains an open problem. The substantial computational cost of directly solving the Boltzmann equation has limited the extent of numerical validation studies to simple, often two-dimensional, flow problems. Recent algorithmic advancements for the Boltzmann–Bhatnagar–Gross–Krook equation introduced by the authors [Dzanic et al., J. Comput. Phys. 486, 112146 (2023)], consisting of a highly efficient high-order spatial discretization augmented with a discretely conservative velocity model, have made it feasible to accurately simulate unsteady three-dimensional flow problems across both the rarefied and continuum regimes. This work presents a comprehensive evaluation and validation of wall boundary conditions across a variety of flow regimes, primarily for the purpose of exploring their effects on momentum transfer in the low Mach limit. Results are presented for a range of steady and unsteady wall-bounded flow problems across both the rarefied and continuum regimes, from canonical two-dimensional laminar flows to unsteady three-dimensional transitional and turbulent flows, the latter of which are the first instances of wall-bounded turbulent flows computed by directly solving the Boltzmann equation. We show that approximations of the molecular gas dynamics equations can accurately predict both non-equilibrium phenomena and complex hydrodynamic flow instabilities and show how spatial and velocity domain resolution affect the accuracy. The results indicate that an accurate approximation of particle transport (i.e., high spatial resolution) is significantly more important than particle collision (i.e., high velocity domain resolution) for predicting flow instabilities and momentum transfer consistent with that predicted by the hydrodynamic equations and that these effects can be computed accurately even with very few degrees of freedom in the velocity domain. These findings suggest that highly accurate spatial schemes (e.g., high-order schemes) are a promising approach for solving molecular gas dynamics for complex flows and that the direct solution of the Boltzmann equation can be performed at a reasonable cost when compared to hydrodynamic simulations at the same level of resolution.