The recent progress in HAXPES combined with Inelastic Background Analysis makes this method a powerful, non-destructive solution to get quantitative information on deeply buried layers and interfaces at depths up to 70 nm. However, we recently highlighted the need for carefully choosing the scattering cross-sections in order to accurately describe the transport of photoelectrons through a complex overlayer structure with layers presenting very different scattering properties. It is found that the transport through such thick bi-layer structures can be described with an effective inelastic scattering cross-section in the form of a weighted sum of individual cross-sections of the pure layers. In this study, we have experimentally investigated this by analyzing Al/Ta/AlGaN stacks on a GaN substrate. We present a refined analytical method, based on the use of a reference spectrum, for determining the required input parameters, i.e. the inelastic mean free path and the effective inelastic scattering cross-section. The use of a reference sample gives extra constraints which make the analysis faster to converge towards a more accurate result. Based on comparisons with TEM, the improved method provides results determined with a deviation typically better than 5% instead of around 10% without reference. The case of much thicker overlayers up to 66 nm is also discussed, notably in terms of accounting for elastic scattering in the analysis. © 2017 Elsevier B.V.