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. (C) 2017 Elsevier B.V. All rights reserved.