Inspired by the motility of small intestine, we investigate the flow generated by a propagating pendular-wave along the walls of a symmetric 2D channel lined with elongated villi-like microstructures. The rigid villi follow simple harmonic axial motion, but with a phase lag to their neighbours, resulting in travelling intervillous contractions. We use lattice Boltzmann simulations to resolve the flow around the villi and the luminal channel space, sampling small to moderate Womersley numbers. We analyse an emergent `mixing' boundary layer in the lumen, separating two distinct flow regions. A mixing region is formed above the villi, characterised by semi-vortical flow patterns, which travel along with the wave. In the channel centre, unidirectional axial flow emerges, flowing opposite to the imposed wave direction, even in the Stokes flow regime. This behaviour contrasts with canonical wave driven peristaltic flow (Jaffrin & Shapiro 1971). The fluid trapped in the intervillous gaps is forced to take a non-reciprocal path due to the travelling pendular-wave, which breaks time-symmetry in the Stokes regime. We propose an effective velocity boundary condition, incorporating perturbations due to the presence of the villi. In the inertial regime, the boundary layer shrinks due to dynamic flow confinement arising from increased oscillatory flow inertia. We identify the Stokes to inertial transition, and find phenomenological scaling laws for the boundary layer decay and axial and radial fluid fluxes. Our results not only advance the understanding of transport within the gut but also suggest a novel way for microfluidic flow control in confined channels.