The aerospace sector is challenged to produce airplanes more efficiently and resiliently in the future. This leads to an increasing demand for improving productivity and flexibility as well as providing solutions for sustainable developments. A bottleneck in production is the machining of large-scale components. Apart from the machining tasks, non-productive operations like fixture adjustment, component handling, referencing and localization are performed within the machining station and can constitute up to 50% of the overall workload. In the UniFix project, Fraunhofer IFAM is participating in the development of a mobile fixture system for large-scale aircraft components, like vertical tail plane and landing flap components of the single aisle aircrafts. By installing components into a mobile holding fixture with an according referencing scheme, a flow line can be established that is composed of specialized workstations discharging the machining station from non-productive processes, leading to higher productivity. This paper focusses on the component localization and referencing strategies for this mobile holding fixture. Here, specific challenges are caused by the transport in between the referencing and the machining process. Therefore, influences that contribute to the overall geometric uncertainty of the referencing process for machining are evaluated in detail. In this work, an automated laser scanner based localization of the components will be presented. Furthermore, estimations on the uncertainty in the involved systems will be conducted and propagated through the localization process.