Absolute position accuracy is the key performance criterion of an Indoor Localization System (ILS). Since ILS are heterogeneous and complex cyber-physical systems, the localization accuracy depends on various influences from the environment, system configuration, and the application processes. To determine the position accuracy of a system in a reproducible, comparable, and realistic manner, these factors must be taken into account. We propose a strategy for analyzing the influences on the position accuracy of ILS using decision trees in combination with application-related or technology-related categorization. The proposed strategy is validated using empirical data from 120 experiments. The accuracy of an Ultra-Wideband and a LiDAR-based ILS was determined under different application-driven influencing factors, considering the application of autonomous mobile robots in warehouses. Finally, the opportunities and limitations of analyzing decision trees to compare system performance, find a suitable system, optimize the environment or system configuration, and understand the relevance of different influencing factors are presented.