Local optima networks (LONs) capture fitness landscape information. They are typically constructed in a black-box manner; information about the problem structure is not utilised. This also applies to the analysis of LONs: knowledge about the problem, such as interaction between variables, is not considered. We challenge this status-quo with an alternative approach: we consider how LON analysis can be improved by incorporating subfunction-based information - this can either be known a-priori or learned during search. To this end, LONs are constructed for several benchmark pseudo-boolean problems using three approaches: firstly, the standard algorithm; a second algorithm which uses deterministic grey-box crossover; and a third algorithm which selects perturbations based on learned information about variable interactions. Metrics related to subfunction changes in a LON are proposed and compared with metrics from previous literature which capture other aspects of a LON. Incorporating problem structure in LON construction and analysing it can bring enriched insight into optimisation dynamics. Such information may be crucial to understanding the difficulty of solving a given problem with state-of-the-art linkage learning optimisers. In light of the results, we suggest incorporation of problem structure as an alternative paradigm in landscape analysis for problems with known or suspected subfunction structure.