Reactive and non-reactiveReynolds-averaged Navier-Stokes (RANS) simulations of hydrogen injection into a confined transverse supersonic flow of vitiated air are conducted. The corresponding conditions were studied in the LAPCAT-II combustor. We consider two operating conditions, which differ in the value of the momentum ratio between the hydrogen and vitiated air inlet streams, thus leading to two distinct values of the equivalence ratio (ER). For its smallest value, smooth combustion develops subject to a preliminary thermal runaway period, while for its largest value, combustion is more strongly intertwined with shock wave dynamics and boundary layer separation. Special emphasis is placed on the possible effects of wall roughness on this reactive flow development. One amongst the conclusions of preliminary computational analyses of the present flowfield was that it may play a significant role on combustion development. This is firmly confirmed in the present study, which takes explicitly the influence of wall roughness into account within the equivalent sand grain modeling framework. For the largest ER value, the combustion stabilization mechanism is found to change dramatically whether roughness is taken into account or not. Its influence is assessed through a detailed comparison with available experimental data.